https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Immacolata+Venditto 2026-05-25T13:36:20Z User contributions MediaWiki 1.35.10 https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13272 2018-08-28T15:24:13Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens'' forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme. ''R. flavefaciens'' CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMiller2009 pmid=19680555<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13271 2018-08-28T15:19:21Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens'' forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens'' CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMiller2009 pmid=19680555<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13270 2018-08-28T15:18:49Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens'' CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMiller2009 pmid=19680555<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13269 2018-08-28T15:18:02Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens'' CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergmillerME2009 pmid=19680555<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13268 2018-08-28T15:17:29Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens'' CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergmillerME2009 pmid=19680555<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13267 2018-08-28T15:16:00Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens'' CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMillerME2009 pmid=19680555<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13266 2018-08-28T15:14:38Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens''CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMillerME2009 pmid=19680555<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13265 2018-08-28T15:13:08Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens''CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMillerME2009 pmid=19680555<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13264 2018-08-28T15:10:59Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. ''R. flavefaciens''forms a multi-enzyme cellulosome complex that plays an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides &lt;cite&gt;BergMiller2009&lt;/cite&gt;. CBMs generally display specificities consistent with the activity of the appended enzyme.''R. flavefaciens''CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt; are components of an enzyme that contains a catalytic module derived from [[GH9]]&lt;cite&gt;VendittoI2016&lt;/cite. The specificity ofCBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]]catalytic module &lt;cite&gt;VendittoI2016&lt;/cite. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> #BergMillerME2009 pmid=19680555<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13261 2018-08-28T14:29:35Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13260 2018-08-28T13:57:58Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13259 2018-08-28T13:55:32Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by [[CBM78]], anyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a [[Carbohydrate-binding_modules#Types|type B]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13258 2018-08-28T13:52:17Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface for a type B glucan binding CBM. It is not a narrow canyon-like structure as displayed by CBM78 butanyway it indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a type B CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13257 2018-08-28T13:43:43Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface that anyway indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a type B CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13256 2018-08-28T13:38:22Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface that anyway indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a type B CBM.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusual solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13255 2018-08-28T13:37:19Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding site located at the concave surface of the protein forms an unusually solvent exposed cleft or planar surface that whenever indicates that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; is a type B CBM.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusual solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13254 2018-08-28T13:24:40Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose <br /> (KA 4.2 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellotetraose, KA 7.0 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellopentaose and KA 4.9 x 10&lt;sup&gt;3&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusual solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13253 2018-08-28T13:14:25Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β-1,4-glucanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantified using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in ''K''&lt;sub&gt;A&lt;/sub&gt; from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusual solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13223 2018-08-24T13:24:29Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantitatively using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13222 2018-08-24T13:23:37Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantitatively using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13221 2018-08-24T13:22:24Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by Isothermal Titration Calorimetry (ITC) and semi-quantitatively using Microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13220 2018-08-24T13:21:21Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from [[GH9]] with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry (ITC) and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13219 2018-08-23T14:20:18Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry (ITC) and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13218 2018-08-23T14:17:48Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module [[GH9]] &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13217 2018-08-23T14:17:04Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module ([[GH9]]) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13216 2018-08-23T14:16:10Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' cite&gt;Bensoussan2017&lt;/cite&gt;. The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module ([[GH9]]) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose &lt;cite&gt;VendittoI2016&lt;/cite&gt;. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13215 2018-08-23T13:59:23Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module GH9. Mutagenesis experiments &lt;cite&gt;VendittoI2016&lt;/cite&gt; confirmed the importance of the aromatic residues in ligand recognition. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13214 2018-08-23T13:57:32Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]] <br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; form a twisted hydrophobic platform &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The concave surface of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;forms an unusually solvent exposed cleft or planar surface &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module GH9. Mutagenesis experiments &lt;cite&gt;VendittoI2016&lt;/cite&gt; confirmed the importance of the aromatic residues in ligand recognition. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13213 2018-08-23T13:37:27Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from ([[GH9]]) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]]<br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1RfGH9 form a twisted hydrophobic platform. In CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, the concave surface forms an unusually solvent exposed cleft or planar surface, with loops connecting β-strands 1 and 2 and β-strands 4 and 5 strongly contributing to the curved topology of β-sheet 2. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition, adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;.<br /> <br /> <br /> == Functionalities == <br /> The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module GH9. Mutagenesis experiments &lt;cite&gt;VendittoI2016&lt;/cite&gt; confirmed the importance of the aromatic residues in ligand recognition. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_79&diff=13212 2018-08-23T13:36:12Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM79.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls &lt;cite&gt;RinconMT2010&lt;/cite&gt;. Two CBM79s (CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79-2&lt;sub&gt;RfGH9&lt;/sub&gt;) were identified in an enzyme that contains a catalytic module derived from GH9 ([[GH9]])with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The ligand binding of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds regenerated (noncrystalline) insoluble cellulose (RC) with a K&lt;sub&gt;A&lt;/sub&gt; of 4.8 x 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; .<br /> <br /> == Structural Features ==<br /> [[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]]<br /> The structure of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å. CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1RfGH9 form a twisted hydrophobic platform. In CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, the concave surface forms an unusually solvent exposed cleft or planar surface, with loops connecting β-strands 1 and 2 and β-strands 4 and 5 strongly contributing to the curved topology of β-sheet 2. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition, adopting a planar orientation in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;.<br /> <br /> <br /> == Functionalities == <br /> The specificity of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; for β-glucans is consistent with endo-β1,4-glucanase activity of catalytic module GH9. Mutagenesis experiments &lt;cite&gt;VendittoI2016&lt;/cite&gt; confirmed the importance of the aromatic residues in ligand recognition. Alanine substitution of Trp606 in CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt;, which is conserved in the CBM family, resulted in complete loss of binding to all ligands. The mutants W564A and W607A retained affinity for barley β-glucan but did not bind xyloglucan. The planar topology of the binding cleft of CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; indicated that this protein may interact with components of insoluble cellulose. ITC and pull down assays showed that CBM79-1&lt;sub&gt;RfGH9&lt;/sub&gt; binds RC &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Alanine substitution of W564 and W606 resulted in loss of binding to RC. The importance of conformation of conserved aromatic residues on CBM specificity is evident in family 2 CBMs that bind to cellulose or xylan &lt;cite&gt;SimpsonPJ2000&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; and CBM79_2&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1&lt;sub&gt;RfGH9&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #SimpsonPJ2000 pmid=10973978<br /> <br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM079]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13211 2018-08-23T13:13:39Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The endo-mode of binding to soluble polysaccharide indicates that CBM80 is [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets (β-sheet 1 and 2) comprising of four anti-parallel β-strands each (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> <br /> CBM80 modules play an enzyme-targeting role that is specific to the ''Ruminococcus'' in a highly complex scaffold &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, a module in an enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #Bensoussan2017 pmid=27712009<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13210 2018-08-23T13:11:46Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The endo-mode of binding to soluble polysaccharide indicates that CBM80 is [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets (β-sheet 1 and 2) comprising of four anti-parallel β-strands each (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> <br /> CBM80 modules play an enzyme-targeting role that is specific to the Ruminococcusin a highly complex scaffold &lt;cite&gt;Bensoussan2017&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, a module in an enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13209 2018-08-23T12:50:37Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The endo-mode of binding to soluble polysaccharide indicates that CBM80 is [[Carbohydrate-binding_modules#Types|type B]] CBM &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets (β-sheet 1 and 2) comprising of four anti-parallel β-strands each (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, a module in an enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13187 2018-08-22T10:32:55Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; [2]. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets (β-sheet 1 and 2) comprising of four anti-parallel β-strands each (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13186 2018-08-22T10:32:00Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; [2]. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets (β-sheet 1 and 2) comprising four anti-parallel β-strands each (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13185 2018-08-22T10:28:32Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; [2]. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13184 2018-08-22T10:24:53Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; [2]. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 104 to 105 M-1, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80 from the ''Ruminococcus flavefaciens'' CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13183 2018-08-22T10:19:37Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; [2]. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 104 to 105 M-1, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13182 2018-08-22T10:16:02Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. The only characterized CBM80 modules are CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;, which are components of enzymes containing catalytic modules derived from GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]) and GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) for CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and GH5_4 ([http://www.cazy.org/GH5_4.html CAZy - GH5_4])for CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; [2]. <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt; display specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, while CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; also binds β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80RfGH5-1/2 binds galactomannan in addition to the β-glucans with affinities in the range of 104 to 105 M-1, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13178 2018-08-22T09:43:13Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 ([http://www.cazy.org/GH5_7.html CAZy - GH5_7]) and GH5_4 catalytic modules ([http://www.cazy.org/GH5_4.html CAZy - GH5_4]), binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13177 2018-08-22T09:42:22Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 [http://www.cazy.org/GH5_7.html CAZy - GH5_7] and GH5_4 catalytic modules [http://www.cazy.org/GH5_4.html CAZy - GH5_4], binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13176 2018-08-22T09:40:51Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 [http://www.cazy.org/GH5_7.html] and GH5_4 catalytic modules [http://www.cazy.org/GH5_4.html], binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13175 2018-08-22T09:34:32Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheet 2) anti-parallel β-strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13174 2018-08-22T09:33:04Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold consisting of two β-sheets comprising four (β-sheet 1) and four (β-sheets) anti-parallel b strands, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13151 2018-08-21T07:51:14Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13150 2018-08-21T07:49:02Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13149 2018-08-20T14:12:54Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial CBM family comprising around 96 amino acids and identified in the ''Ruminococcus flavefaciens'' cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity &lt;cite&gt;VendittoI2016&lt;/cite&gt; CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;, additionally, this CBM binds mannotetraose and not cellotetraose &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl labelled protein. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) apo, and in complex with mannohexaose and cellohexaose, was solved with resolutions of 1.0 Å, 1.4 Å and 1.5 Å, respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans. Other examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families [[CBM16]] &lt;cite&gt;BaeB2008&lt;/cite&gt; and [[CBM29]] &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from ''Ruminococcus flavefaciens'' &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13145 2018-08-10T11:24:11Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial family comprising around 96 amino acids and identified in the Ruminococcus flavefaciens cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;. Additionally, this CBM binds mannotetraose and not cellotetraose.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein. The apo structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; (Figure 1) and in complex with mannohexaose and cellohexaose was solved to a resolution of 1.0 Å, 1.4 Å and 1.5 Å respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans. Examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families CBM16 &lt;cite&gt;BaeB2008&lt;/cite&gt; and CBM29 &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from Ruminococcus flavefaciens &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_80&diff=13144 2018-08-10T11:23:06Z

<p>Immacolata Venditto: </p> <hr /> <div>&lt;!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --&gt;<br /> {{UnderConstruction}}<br /> * [[Author]]: ^^^Immacolata Venditto^^^<br /> * [[Responsible Curator]]: ^^^Harry Gilbert^^^<br /> ----<br /> <br /> &lt;!-- The data in the table below should be updated by the Author/Curator according to current information on the family --&gt;<br /> &lt;div style=&quot;float:right&quot;&gt;<br /> {| {{Prettytable}} <br /> |-<br /> |{{Hl2}} colspan=&quot;2&quot; align=&quot;center&quot; |'''CAZy DB link'''<br /> |-<br /> | colspan=&quot;2&quot; |{{CAZyDBlink}}CBM80.html<br /> |}<br /> &lt;/div&gt;<br /> &lt;!-- This is the end of the table --&gt;<br /> <br /> == Ligand specificities ==<br /> CBM80 is a small bacterial family comprising around 96 amino acids and identified in the Ruminococcus flavefaciens cellulosome &lt;cite&gt;RinconMT2010&lt;/cite&gt;. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;, and CBM80&lt;sub&gt;RfGH5&lt;/sub&gt;) with endo-β1,4-glucanases activity. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity. The only family member characterized is CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; binds galactomannan in addition to the β-glucans with affinities in the range of 10&lt;sup&gt;4&lt;/sup&gt; to 10&lt;sup&gt;5&lt;/sup&gt; M&lt;sup&gt;-1&lt;/sup&gt;. Additionally, this CBM binds mannotetraose and not cellotetraose.<br /> <br /> == Structural Features ==<br /> [[File:CBM80.jpg|thumb|300px|right|'''Figure 1.''' Crystal structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt;. The residues that contribute to ligand recognition are shown.]]<br /> The three-dimensional structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; ([{{PDBlink}}5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein. The apo structure of CBM80&lt;sub&gt;RfGH51/2&lt;/sub&gt; (Figure 1) and in complex with mannohexaose and cellohexaose was solved to a resolution of 1.0 Å, 1.4 Å and 1.5 Å respectively &lt;cite&gt;VendittoI2016&lt;/cite&gt;. CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The β-sheet 2 of CBM80&lt;sub&gt;RfGH-5-1/2&lt;/sub&gt; presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose-CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 &lt;cite&gt;VendittoI2016&lt;/cite&gt;. The structure of CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; in complex with cellohexaose revealed electron density for only three glucose units &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == Functionalities == <br /> CBM80, component of enzyme that contains GH5_7 and GH5_4 catalytic modules, binds β-glucans and β-mannans. Examples of CBMs that recognize both β-1,4-glucans and β-1,4-mannans are found in families CBM16 &lt;cite&gt;BaeB2008&lt;/cite&gt; and CBM29 &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The key residues implicated in ligand binding were identified by site-direct mutagenesis. Alanine substitution of Trp453 and Trp489 revealed a complete abrogation of binding to β-glucans and β-mannans, showing the importance of tryptophan residues in ligand recognition. CBMs that bind to β-1,4-glycans typically contain three aromatic residues that make apolar interactions with sugars &lt;cite&gt;CharnockSJ2002&lt;/cite&gt;. The predicted polar interactions between the protein and β-glycans have very little influence on affinity. <br /> <br /> == Family Firsts ==<br /> ;First Identified: CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; from Ruminococcus flavefaciens &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> ;First Structural Characterization: The first 3D crystal structure solved was CBM80&lt;sub&gt;RfGH5-1/2&lt;/sub&gt; &lt;cite&gt;VendittoI2016&lt;/cite&gt;.<br /> <br /> == References ==<br /> &lt;biblio&gt;<br /> #RinconMT2010 pmid=20814577<br /> #VendittoI2016 pmid=27298375<br /> #BaeB2008 pmid=18025086<br /> #CharnockSJ2002 pmid=12391332<br /> &lt;/biblio&gt;<br /> <br /> [[Category:Carbohydrate Binding Module Families|CBM080]]</div>

Immacolata Venditto https://www.cazypedia.org/index.php?title=File:CBM80.jpg&diff=13142 2018-08-08T14:48:38Z

<p>Immacolata Venditto: Immacolata Venditto uploaded a new version of File:CBM80.jpg</p> <hr /> <div></div>

Immacolata Venditto