Carbohydrate Binding Module Family 62 - Revision history

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

2021-12-18T21:14:59Z

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

Elizabeth Ficko-Blean: /* Structural Features */

2018-03-06T16:22:03Z

Structural Features

Harry Gilbert: /* Structural Features */

2018-02-05T22:52:14Z

Structural Features

Harry Brumer: /* Structural Features */

2015-02-23T17:54:33Z

Structural Features

Harry Gilbert at 17:39, 23 February 2015

2015-02-23T17:39:24Z

Harry Brumer: /* Functionalities */

2015-02-23T16:28:33Z

Functionalities

Harry Brumer: /* Ligand specificities */

2015-02-23T16:24:42Z

Ligand specificities

Harry Gilbert at 14:23, 20 February 2015

2015-02-20T14:23:52Z

Harry Gilbert at 17:50, 30 January 2015

2015-01-30T17:50:13Z

Harry Gilbert at 17:46, 30 January 2015

2015-01-30T17:46:49Z

@@ 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]]: ^^^Cedric Montanier^^^
+* [[Author]]: [[User:Cedric Montanier|Cedric Montanier]]
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
+* [[Responsible Curator]]:  [[User:Harry Gilbert|Harry Gilbert]]
 ----

@@ Line 25: / Line 25: @@
 The structure of ''Ct''CBM62 comprises residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.
-The ligand binding site is formed by the loops on top of the β-jelly-roll, comprising a pocket ≈ 7.5 Å wide and ≈ 5 Å deep. ''Ct''CBM62 is thus a type C CBM. The galactopyranose moiety of both xyloglucan oligosaccharides and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in the shallow binding pocket, while the indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring makes a polar contact with NH2 of Arg 65 and the backbone O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but the O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl of C2 is hydrogen bonded only to the OH of Tyr 68.
+The ligand binding site is formed by the loops on top of the β-jelly-roll, comprising a pocket ≈ 7.5 Å wide and ≈ 5 Å deep. ''Ct''CBM62 is thus a [[Carbohydrate-binding_modules#Types|type C]] CBM. The galactopyranose moiety of both xyloglucan oligosaccharides and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in the shallow binding pocket, while the indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring makes a polar contact with NH2 of Arg 65 and the backbone O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but the O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl of C2 is hydrogen bonded only to the OH of Tyr 68.
 == Functionalities ==

@@ Line 25: / Line 25: @@
 The structure of ''Ct''CBM62 comprises residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.
-The ligand binding site is formed by the loops on top of the β-jelly-roll, comprising a pocket ≈ 7.5 Å wide and ≈ 5 Å deep. ''Ct''CBM62 is thus a type C CBM.
+The ligand binding site is formed by the loops on top of the β-jelly-roll, comprising a pocket ≈ 7.5 Å wide and ≈ 5 Å deep. ''Ct''CBM62 is thus a type C CBM. The galactopyranose moiety of both xyloglucan oligosaccharides and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in the shallow binding pocket, while the indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring makes a polar contact with NH2 of Arg 65 and the backbone O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but the O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl of C2 is hydrogen bonded only to the OH of Tyr 68.
 == Functionalities ==

@@ Line 23: / Line 23: @@
 == Structural Features ==
-The structure of ''Ct''CBM62 comprisesresidues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.
+The structure of ''Ct''CBM62 comprises residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.
 The ligand binding site is formed by the loops on top of the β-jelly-roll, comprising a pocket ≈ 7.5 Å wide and ≈ 5 Å deep. ''Ct''CBM62 is thus a type C CBM.
 The galactopyranose moiety of both xyloglucan oligosaccharides and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in the shallow binding pocket, while the indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring makes a polar contact with NH2 of Arg 65 and the backbone O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but the O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl of C2 is hydrogen bonded only to the OH of Tyr 68.
 == Functionalities ==

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-The only known crystallographic structure of a carbohydrate-binding module of family 62 is ''Ct''CBM62. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. These sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and α-L-arabinopyranose and α-D-galactopyranose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for both galactose and arabinopyranose, as opposed to mannose, glucose and xylose.
+The only known crystallographic structure of a carbohydrate-binding module of family 62 is ''Ct''CBM62. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. These crystal structures of ''Ct''CBM62 in complex with its ligands revealed that the interactions between the protein and α-L-arabinopyranose and α-D-galactopyranose are highly conserved. The data showed that an axial O4 is a key determinant for the specificity of ''Ct''CBM62, explaining why the ligand binding pocket targets galactose and arabinopyranose, as opposed to mannose, glucose and xylose.
-Isothermal titration calorimetry revealed affinity for a wide range of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. The ligand-binding site is located in the the loops that connect the β-sheets. ''Ct''CBM62 recognises the non-reducing terminal sugars of oligosaccharides and polysaccharides.
+Isothermal titration calorimetry revealed affinity for a wide range of galactose and/or arabinose containing polysaccharides such as galactomannan, tamarind xyloglucan, arabinogalactan and arabinan. The ligand-binding site is located in the the loops that connect the β-sheets. ''Ct''CBM62 recognises the non-reducing terminal sugars (arabinopyranose or galactose) of oligosaccharides and polysaccharides.
 == Structural Features ==
-The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.
+The structure of ''Ct''CBM62 comprisesresidues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.
-''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.
+The ligand binding site is formed by the loops on top of the β-jelly-roll, comprising a pocket ≈ 7.5 Å wide and ≈ 5 Å deep. ''Ct''CBM62 is thus a type C CBM.
-The galactopyranose moiety of both xyloglucan oligosaccharides and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while the indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.
+The galactopyranose moiety of both xyloglucan oligosaccharides and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in the shallow binding pocket, while the indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring makes a polar contact with NH2 of Arg 65 and the backbone O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but the O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl of C2 is hydrogen bonded only to the OH of Tyr 68.
 == Functionalities ==
-''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose.
+''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides containing terminal D-galactose or L-arabinopyranose residues.
-It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ca. 200-fold more tightly to the galactosyl side-chains of galactomannan, and ca. 100-fold more tightly to xyloglucan, than to galactose.  Such increased binding to multivalent ligands is a classic example of avidity effects <cite>Boraston2002 Vijayan1999</cite>.
+It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ca. 200- and 100-fold more tightly to the galactosyl side-chains of galactomannan and xyloglucan, respectively, compared to galactose.  Such increased binding to multivalent ligands is a classic example of avidity effects <cite>Boraston2002 Vijayan1999</cite>.
 == Family Firsts ==

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.
+The only known crystallographic structure of a carbohydrate-binding module of family 62 is ''Ct''CBM62. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. These sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and -<sub>D</sub> galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for both galactose and arabinopyranose, as opposed to mannose, glucose and xylose.
-Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.
+Isothermal titration calorimetry revealed affinity for a wide range of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. The ligand-binding site is located in the the loops that connect the β-sheets. ''Ct''CBM62 recognises the non-reducing terminal sugars of oligosaccharides and polysaccharides.
@@ Line 32: / Line 32: @@
 == Functionalities ==
-''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.
+''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose.
 It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects <cite>Boraston2002,Vijayan1999</cite>.