Carbohydrate Binding Module Family 79 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:19:31Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Elizabeth Ficko-Blean at 08:59, 30 August 2018

2018-08-30T08:59:22Z

Harry Brumer at 18:22, 29 August 2018

2018-08-29T18:22:36Z

Elizabeth Ficko-Blean at 09:49, 29 August 2018

2018-08-29T09:49:47Z

Elizabeth Ficko-Blean at 09:48, 29 August 2018

2018-08-29T09:48:19Z

Elizabeth Ficko-Blean at 09:35, 29 August 2018

2018-08-29T09:35:13Z

Elizabeth Ficko-Blean at 09:33, 29 August 2018

2018-08-29T09:33:59Z

Elizabeth Ficko-Blean at 08:11, 29 August 2018

2018-08-29T08:11:16Z

Elizabeth Ficko-Blean at 08:07, 29 August 2018

2018-08-29T08:07:52Z

Elizabeth Ficko-Blean at 07:55, 29 August 2018

2018-08-29T07:55:28Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Immacolata Venditto^^^
+* [[Author]]: [[User:Immacolata Venditto|Immacolata Venditto]]
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
+* [[Responsible Curator]]:  [[User:Harry Gilbert|Harry Gilbert]]
 ----

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: ^^^Immacolata Venditto^^^
 * [[Responsible Curator]]:  ^^^Harry Gilbert^^^

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 == Structural Features ==
-[[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.'''  Crystal structure of CBM79-1<sub>RfGH9</sub>. ([{{PDBlink}}4V1L PDB ID 4V1L])([{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]]
+[[File:CBM79-1.jpg|thumb|300px|right|'''Figure 1.'''  Crystal structure of CBM79-1<sub>RfGH9</sub>. ([{{PDBlink}}4V1L PDB ID 4V1L], [{{PDBlink}}4V1K PDB ID 4V1K]). The aromatic residues that contribute to ligand recognition are shown.]]
 The structure of CBM79-1<sub>RfGH9</sub>  was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å <cite>VendittoI2016</cite>. CBM79-1<sub>RfGH9</sub> displays a beta-sandwich fold in which the 12 antiparallel β-strands are organized in two β-sheets 1 and 2 (Figure 1) <cite>VendittoI2016</cite>. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature <cite>VendittoI2016</cite>. The ligand binding site located at the concave surface of the protein forms an unusual solvent exposed cleft/planar surface for a [[Carbohydrate-binding_modules#Types|type B]]  β-glucan binding CBM. It is not a narrow canyon-like structure  as displayed by [[CBM78]]. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1<sub>RfGH9</sub> form a twisted hydrophobic platform within the cleft <cite>VendittoI2016</cite>. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition adopting a planar orientation in CBM79-1<sub>RfGH9</sub> <cite>VendittoI2016</cite>.

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 == Functionalities ==
-CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' <cite>Bensoussan2017</cite>. ''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 <cite>BergMiller2009</cite>. CBMs generally display specificities consistent with the activity of the appended enzyme. ''R. flavefaciens'' CBM79-1<sub>RfGH9</sub> and CBM79-2<sub>RfGH9</sub> are components of an enzyme that contains a [[GH9]] catalytic module <cite>VendittoI2016</cite>. The specificity of CBM79-1<sub>RfGH9</sub> for β-glucans is consistent with endo-β1,4-glucanase activity of the [[GH9]] catalytic module <cite>VendittoI2016</cite>.
+CBM79 fulfills an enzyme-targeting role that is specific to ''Ruminococcus'' <cite>Bensoussan2017</cite>. ''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 <cite>BergMiller2009</cite>. CBMs generally display specificities consistent with the activity of the appended enzyme. ''R. flavefaciens'' CBM79-1<sub>RfGH9</sub> and CBM79-2<sub>RfGH9</sub> are components of an enzyme that contains a [[GH9]] catalytic module <cite>VendittoI2016</cite>. The specificity of CBM79-1<sub>RfGH9</sub> for β-glucans is consistent with targeting the endo-β1,4-glucanase activity of the [[GH9]] catalytic module to its substrate <cite>VendittoI2016</cite>.
 == Family Firsts ==

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 == Ligand specificities ==
 ''Ruminococcus flavefaciens'' is an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls <cite>RinconMT2010</cite>. CBM79 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome.  Two CBM79s (CBM79-1<sub>RfGH9</sub> and CBM79-2<sub>RfGH9</sub>)  were identified in an enzyme that contains a [[GH9]]  catalytic module with endo-β-1,4-glucanase activity <cite>VendittoI2016</cite>. Both CBM79s bind to a range of β-1,4- and mixed-linked β-1,3-1,4-glucans <cite>VendittoI2016</cite>. The ligand binding of CBM79-1<sub>RfGH9</sub> was quantified by Isothermal Titration Calorimetry (ITC) and  semi-quantified using Microarrays <cite>VendittoI2016</cite>. CBM79-1<sub>RfGH9</sub> binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities of 10<sup>4</sup> M<sup>-1</sup> <cite>VendittoI2016</cite>. The small increase in ''K''<sub>A</sub> from cellotetraose to cellohexaose
-(''K''<sub>A</sub> 4.2 x 10<sup>3</sup> M<sup>-1</sup> for cellotetraose, ''K''<sub>A</sub> 7.0 x 10<sup>3</sup> M<sup>-1</sup> for cellopentaose and ''K''<sub>A</sub> 4.9 x 10<sup>3</sup> M<sup>-1</sup> for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites <cite>VendittoI2016</cite>. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains <cite>VendittoI2016</cite>. CBM79-1<sub>RfGH9</sub> binds regenerated (noncrystalline) insoluble cellulose (RC) with a  ''K''<sub>A</sub> of 4.8 x 10<sup>4</sup> M<sup>-1</sup> <cite>VendittoI2016</cite>. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition <cite>VendittoI2016</cite>. Alanine substitution of Trp606 in CBM79-1<sub>RfGH9</sub>, which is conserved in the CBM family, resulted in complete loss of binding to all ligands <cite>VendittoI2016</cite>. The mutants Trp564A and Trp607A retained affinity for barley β-glucan but did not bind xyloglucan <cite>VendittoI2016</cite>. Alanine substitution of Trp564 and Trp606 resulted in loss of binding to RC <cite>VendittoI2016</cite>. The importance of conformation of conserved aromatic residues on CBM specificity is evident in [[CBM2]] members that bind to cellulose or xylan <cite>SimpsonPJ2000</cite>. CBM79 binding to non-crystalline polysaccharides indicates that CBM79-1<sub>RfGH9</sub> is a [[Carbohydrate-binding_modules#Types|type B]] CBM <cite>VendittoI2016</cite>.
+(''K''<sub>A</sub> 4.2 x 10<sup>3</sup> M<sup>-1</sup> for cellotetraose, ''K''<sub>A</sub> 7.0 x 10<sup>3</sup> M<sup>-1</sup> for cellopentaose and ''K''<sub>A</sub> 4.9 x 10<sup>3</sup> M<sup>-1</sup> for cellohexaose) suggests that ligand recognition is dominated by four sugar binding sites <cite>VendittoI2016</cite>. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains <cite>VendittoI2016</cite>. CBM79-1<sub>RfGH9</sub> binds regenerated (non-crystalline) insoluble cellulose (RC) with a  ''K''<sub>A</sub> of 4.8 x 10<sup>4</sup> M<sup>-1</sup> <cite>VendittoI2016</cite>. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition <cite>VendittoI2016</cite>. Alanine substitution of Trp606 in CBM79-1<sub>RfGH9</sub>, which is conserved in the CBM family, resulted in complete loss of binding to all ligands <cite>VendittoI2016</cite>. The mutants Trp564A and Trp607A retained affinity for barley β-glucan but did not bind xyloglucan <cite>VendittoI2016</cite>. Alanine substitution of Trp564 and Trp606 resulted in loss of binding to RC <cite>VendittoI2016</cite>. The importance of conformation of conserved aromatic residues on CBM specificity is evident in [[CBM2]] members that bind to cellulose or xylan <cite>SimpsonPJ2000</cite>. CBM79 binding to non-crystalline polysaccharides indicates that CBM79-1<sub>RfGH9</sub> is a [[Carbohydrate-binding_modules#Types|type B]] CBM <cite>VendittoI2016</cite>.
 == Structural Features ==

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 == Family Firsts ==
-;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1<sub>RfGH9</sub> and CBM79_2<sub>RfGH9</sub>  <cite>VendittoI2016</cite>.
+;First Identified: CBM79 from the ''Ruminococcus flavefaciens'' CBM79_1<sub>RfGH9</sub> and CBM79_2<sub>RfGH9</sub> were the first CBM79 members characterized <cite>VendittoI2016</cite>.
 ;First Structural Characterization: The first available crystal structure and the first complex structure of a CBM79 is from CBM79_1<sub>RfGH9</sub> <cite>VendittoI2016</cite>.