Carbohydrate Binding Module Family 86 - Revision history

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

2021-12-18T21:20:16Z

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

Harry Brumer: /* Structural Features */ Added some intrawiki links

2020-02-14T16:55:49Z

Structural Features: Added some intrawiki links

Elizabeth Ficko-Blean at 14:14, 13 February 2020

2020-02-13T14:14:17Z

Maria Louise Leth at 08:25, 13 February 2020

2020-02-13T08:25:26Z

Harry Brumer: standardized PDB links

2020-02-07T17:30:14Z

standardized PDB links

Harry Brumer: minor formatting clean-up

2020-02-07T17:27:20Z

minor formatting clean-up

Harry Brumer: minor formatting clean-up

2020-02-07T17:25:57Z

minor formatting clean-up

Maria Louise Leth at 13:38, 6 February 2020

2020-02-06T13:38:52Z

Maria Louise Leth at 12:54, 6 February 2020

2020-02-06T12:54:32Z

Elizabeth Ficko-Blean at 09:42, 4 February 2020

2020-02-04T09:42:41Z

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Maria Louise Leth^^^
+* [[Author]]: [[User:Maria Louise Leth|Maria Louise Leth]]
-* [[Responsible Curator]]:  ^^^Maher Abou Hachem^^^
+* [[Responsible Curator]]:  [[User:Maher Abou Hachem|Maher Abou Hachem]]
 ----

@@ Line 21: / Line 21: @@
 == Structural Features ==
-The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([{{PDBlink}}6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan <cite>Leth2018</cite>. W42 contributes in addition to affinity, but to a lesser extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand <cite>Szabo</cite> or employ Ca<sup>2+</sup> to mediate ligand binding <cite>Jamal</cite>.
+The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([{{PDBlink}}6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan <cite>Leth2018</cite>. W42 contributes in addition to affinity, but to a lesser extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand (e.g., [[CBM15]]) <cite>Szabo</cite>  or employ Ca<sup>2+</sup> to mediate ligand binding (e.g., [[CBM36]]) <cite>Jamal</cite>.
-−
 == Functionalities ==
 Members of family CBM86 are exclusively located in the N-terminal of GH10 xylanases from the Clostridiales order of Firmicutes, where it is often associated with additional CBM modules from family 9 and 22. It recognizes both xylan and xylo-oligosaccharides<cite>Leth2018 Leth2019</cite>. The truncation of this module from ''Ri''Xyn10A resulted in about two fold higher ''K''<sub>m</sub> and a similar increase in ''k''<sub>cat</sub>, suggesting that this module contributes to xylan affinity and xylan capture <cite>Leth2018</cite>.

@@ Line 21: / Line 21: @@
 == Structural Features ==
-The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([{{PDBlink}}6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand <cite>Szabo</cite> or employ Ca<sup>2+</sup> to mediate ligand binding <cite>Jamal</cite>.
+The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([{{PDBlink}}6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan <cite>Leth2018</cite>. W42 contributes in addition to affinity, but to a lesser extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand <cite>Szabo</cite> or employ Ca<sup>2+</sup> to mediate ligand binding <cite>Jamal</cite>.
 == Functionalities ==
@@ Line 27: / Line 27: @@
 == Family Firsts ==
-;First Identified
+;First Identified: Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82 <cite>Leth2018</cite>.
-Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82 <cite>Leth2018</cite>.
+;First Structural Characterization: The first crystal structure of the family CBM86 is ''Ri''CBM86 ([{{PDBlink}}6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A <cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.
 == References ==

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: ^^^Maria Louise Leth^^^
 * [[Responsible Curator]]:  ^^^Maher Abou Hachem^^^

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-[[File:cbm86 fig1.png|thumb|300px|right| '''Figure 1''' A) Domain organization of the xylanase ''Ri''Xyn10A from ''R. intestinalis''. Grey module: signal peptide, light green module: BIG2, bacterial immunoglobulin-like domain group 2, dark green domain: LBR, Listeria-Bacteriodes repeat domain, and AA: amino acids. B) Architecture of the shallow binding site. C) Crystal structure of ''Ri''CBM86 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) with the four visible xylosyl residues of the xylohexaose ligand. The aromatic residues and the residues contributing to direct hydrogen bonding are shown as sticks in green.]]
+[[File:cbm86 fig1.png|thumb|300px|right| '''Figure 1''' A) Domain organization of the xylanase ''Ri''Xyn10A from ''R. intestinalis''. Grey module: signal peptide, light green module: BIG2, bacterial immunoglobulin-like domain group 2, dark green domain: LBR, Listeria-Bacteriodes repeat domain, and AA: amino acids. B) Architecture of the shallow binding site. C) Crystal structure of ''Ri''CBM86 ([{{PDBlink}}6SGF PDB: 6SGF]) with the four visible xylosyl residues of the xylohexaose ligand. The aromatic residues and the residues contributing to direct hydrogen bonding are shown as sticks in green.]]
 The CBM86 family was first described in 2018. The founding member, ''Ri''CBM86, was identified in a modular GH10 xylanase from the human gut bacteria ''Roseburia intestinalis'' L1-82 <cite>Leth2018</cite>. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (''K''<sub>D</sub>=479 µM), followed by xylopentaose (''K''<sub>D</sub>=490 µM), xylotetraose (''K''<sub>D</sub>=998 µM), and xylotriose (''K''<sub>D</sub>=1900 µM) <cite>Leth2018</cite>. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (''K''<sub>D</sub>=0.02 mg ml<sup>-1</sup>) compared to birch glucuronoxylan (''K''<sub>D</sub>=0.6 mg ml<sup>-1</sup>) <cite>Leth2018</cite>. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides <cite>Leth2019</cite>.
 == Structural Features ==
-The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand <cite>Szabo</cite> or employ Ca<sup>2+</sup> to mediate ligand binding <cite>Jamal</cite>.
+The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([{{PDBlink}}6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand <cite>Szabo</cite> or employ Ca<sup>2+</sup> to mediate ligand binding <cite>Jamal</cite>.
 == Functionalities ==
@@ Line 30: / Line 30: @@
 Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82 <cite>Leth2018</cite>.
 ;First Structural Characterization
-The first crystal structure of the family CBM86 is ''Ri''CBM86 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A<cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.
+The first crystal structure of the family CBM86 is ''Ri''CBM86 ([{{PDBlink}}6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A <cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.
 == References ==

@@ Line 19: / Line 19: @@
 == Ligand specificities ==
 The CBM86 family was first described in 2018. The founding member, ''Ri''CBM86, was identified in a modular GH10 xylanase from the human gut bacteria ''Roseburia intestinalis'' L1-82<cite>Leth2018</cite>. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (''K''<sub>D</sub>=479 µM), followed by xylopentaose (''K''<sub>D</sub>=490 µM), xylotetraose (''K''<sub>D</sub>=998 µM), and xylotriose (''K''<sub>D</sub>=1900 µM)<cite>Leth2018</cite>. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (''K''<sub>D</sub>=0.02 mg ml<sup>-1</sup>) compared to birch glucuronoxylan (''K''<sub>D</sub>=0.6 mg ml<sup>-1</sup>)<cite>Leth2018</cite>. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides<cite>Leth2019</cite>.
 == Structural Features ==
-The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF])<cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding<cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand or employ Ca<sup>2+</sup> to mediate ligand binding<cite>Jamal</cite>.
+The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF])<cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding<cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand<cite>Szabo</cite> or employ Ca<sup>2+</sup> to mediate ligand binding<cite>Jamal</cite>.
@@ Line 40: / Line 42: @@
 #Leth2019 pmid=31693302
 #Jamal pmid=15242594

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.
+The CBM86 family was first described in 2018. The founding member, ''Ri''CBM86, was identified in a modular GH10 xylanase from the human gut bacteria ''Roseburia intestinalis'' L1-82<cite>Leth2018</cite>. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (''K''<sub>D</sub>=479 µM), followed by xylopentaose (''K''<sub>D</sub>=490 µM), xylotetraose (''K''<sub>D</sub>=998 µM), and xylotriose (''K''<sub>D</sub>=1900 µM)<cite>Leth2018</cite>. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (''K''<sub>D</sub>=0.02 mg ml<sup>-1</sup>) compared to birch glucuronoxylan (''K''<sub>D</sub>=0.6 mg ml<sup>-1</sup>)<cite>Leth2018</cite>. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides<cite>Leth2019</cite>.
 == Structural Features ==
-''Content in this section should include, in paragraph form, a description of:''
+The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF])<cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent.  The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding<cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand or employ Ca<sup>2+</sup> to mediate ligand binding<cite>Jamal</cite>.
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+Members of family CBM86 are exclusively located in the N-terminal of GH10 xylanases from the Clostridiales order of Firmicutes, where it is often associated with additional CBM modules from family 9 and 22. It recognizes both xylan and xylo-oligosaccharides<cite>Leth2018 Leth2019</cite>. The truncation of this module from ''Ri''Xyn10A resulted in about two fold higher ''K''<sub>m</sub> and a similar increase in ''k''<sub>cat</sub>, suggesting that this module contributes to xylan affinity and xylan capture<cite>Leth2018</cite>.
 == Family Firsts ==
 ;First Identified
-:Insert archetype here, possibly including ''very brief'' synopsis.
+Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82<cite>Leth2018</cite>.
 ;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+The first crystal structure of the family CBM86 is ''Ri''CBM86 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A<cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Leth2018 pmid=29610517
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
-#Boraston2004 pmid=15214846
+#Leth2019 pmid=31693302
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
+#Jamal pmid=15242594
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM086]] <!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. -->