Carbohydrate Binding Module Family 15 - Revision history

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

2021-12-18T21:19:09Z

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

Elizabeth Ficko-Blean at 16:03, 6 March 2018

2018-03-06T16:03:39Z

Harry Gilbert: /* Family Firsts */

2018-02-07T16:43:00Z

Family Firsts

Harry Gilbert: /* Structural Features */

2018-02-07T16:42:33Z

Structural Features

Harry Gilbert: /* Ligand specificities */

2018-02-07T16:41:02Z

Ligand specificities

Harry Gilbert: /* Structural Features */

2018-02-05T22:38:34Z

Structural Features

Harry Gilbert: /* Structural Features */

2018-02-05T22:38:17Z

Structural Features

Harry Brumer: /* Family Firsts */

2018-01-31T19:06:02Z

Family Firsts

Harry Brumer: /* Family Firsts */

2018-01-31T19:05:14Z

Family Firsts

Elizabeth Ficko-Blean at 12:35, 17 January 2018

2018-01-17T12:35:21Z

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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]]: ^^^Harry Gilbert^^^
+* [[Author]]: [[User:Harry Gilbert|Harry Gilbert]]
-* [[Responsible Curator]]:  ^^^Elizabeth Ficko-Blean^^^
+* [[Responsible Curator]]:  [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]
 ----

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 == Ligand specificities ==
-The three family 15 CBMs (CBM15s) are all derived from the ''Cellvibrio'' bacterial genus. The one fully characterized CBM15 module was from ''Cellvibrio japonicus'' Xyl10C <cite>Szabo2001</cite> bound to different forms of xylan with a preference for oat spelt xylan (''K''<sub>A</sub> of ~1.4 x 10<sup>4</sup> M<sup>-1</sup>). The CBM also bound to xylooligosacchrides exhibiting affinities for xylohexaose and xylopentaose that were similar to oat spelt xylan, and significantly weaker affinity for xylotetraose and xylotriose.   The protein displayed weak but measurable affinity (KA of ~2 x 10<sup>3</sup> M<sup>-1</sup>) for barley &beta;1,3-&beta;1,4-mixed linked glucan and cellohexaose. The CBM15 module did not bind to insoluble xylan or amorphous cellulose. Isothermal titration calorimetry showed that binding to xylan and glucan ligands was driven by enthalpic forces with changes in entropy have a negative impact on affinity <cite>Szabo2001</cite>. The stoichiometry of binding to soluble xylans was consistent with an endo binding mode, demonstrating that the family 15 module is a type B CBM.
+The three family 15 CBMs (CBM15s) are all derived from the ''Cellvibrio'' bacterial genus. The one fully characterized CBM15 module was from ''Cellvibrio japonicus'' Xyl10C <cite>Szabo2001</cite> bound to different forms of xylan with a preference for oat spelt xylan (''K''<sub>A</sub> of ~1.4 x 10<sup>4</sup> M<sup>-1</sup>). The CBM also bound to xylooligosacchrides exhibiting affinities for xylohexaose and xylopentaose that were similar to oat spelt xylan, and significantly weaker affinity for xylotetraose and xylotriose.   The protein displayed weak but measurable affinity (KA of ~2 x 10<sup>3</sup> M<sup>-1</sup>) for barley &beta;1,3-&beta;1,4-mixed linked glucan and cellohexaose. The CBM15 module did not bind to insoluble xylan or amorphous cellulose. Isothermal titration calorimetry showed that binding to xylan and glucan ligands was driven by enthalpic forces with changes in entropy have a negative impact on affinity <cite>Szabo2001</cite>. The stoichiometry of binding to soluble xylans was consistent with an endo binding mode, demonstrating that the family 15 module is a [[Carbohydrate-binding_modules#Types|type B]] CBM.
 == Structural Features ==

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 == Family Firsts ==
-;First Identified: The first CBM15 was observed in the ''Cellvibrio mixtus'' GH10 xylanase XylB, and qualitative studies indicated that the protein module bound to glucans <cite>Millward-Sadler1995</cite>.   The first detailed analysis of a CBM15 was from the ''C. japonicus'' xylanase Xyn10C <cite>Szabo2001</cite>.
+;First Identified: The first member of CBM15 was observed in the ''Cellvibrio mixtus'' GH10 xylanase XylB, and qualitative studies indicated that the protein module bound to glucans <cite>Millward-Sadler1995</cite>.   The first detailed analysis of a CBM15 was from the ''C. japonicus'' xylanase Xyn10C <cite>Szabo2001</cite>.
-;First Structural Characterization: The first 3D structure of a CBM15 was determined by X-ray crystallography from the ''C. japonicus'' xylanase Xyn10A <cite>Szabo2001</cite>. This also represents the first structure of a xylan binding CBM in complex with its ligand.
+;First Structural Characterization: The first 3D structure of a CBM15 module was determined by X-ray crystallography from the ''C. japonicus'' xylanase Xyn10A <cite>Szabo2001</cite>. This also represents the first structure of a xylan binding CBM in complex with its ligand.
 == References ==

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 [[File:CBM15structure.png|thumb|300px|right|'''Figure 1.'''  The fold of the CBM15 in ''C. japonicus'' Xyn10C (see [{{PDBlink}}1GNY PDB ID 1GNY]) highlighting the two perpendicular tryptophans bound to xylose residues n and n+2 in the 3-fold helical structure of xylan.]]
-CBM15s comprise ~150 amino acids. The crystal structure of the protein module from the ''C. japonicus'' GH10 xylanase Xyn10C was determined in complex with xylohexaose <cite>Szabo2001</cite>. The structure of CBM15 forms a classic &beta;-jelly roll, predominantly consisting of five major anti-parallel &beta;-strands on the two faces CBM15 contains a deep cleft that runs along the concave face of the &beta;-sheet, 20–25 Å long, which forms the binding site for the target ligands.
+CBM15 modules comprise ~150 amino acids. The crystal structure of the protein module from the ''C. japonicus'' GH10 xylanase Xyn10C was determined in complex with xylohexaose <cite>Szabo2001</cite>. The structure of the CBM15 member forms a classic &beta;-jelly roll, predominantly consisting of five major anti-parallel &beta;-strands on the two faces. The CBM15 module contains a deep cleft that runs along the concave face of the &beta;-sheet, 20–25 Å long, which forms the binding site for the target ligands.
 The protein was crystallized in the presence of xylohexaose, and the structure reveals five well-ordered xylose rings (defined as Xyl1 to Xyl5 from the reducing to non-reducing end). Two solvent-exposed tryptophan residues, Trp176 and Trp181, lie in the binding groove and make hydrophobic stacking interactions with Xyl2 and Xyl4, respectively.  The indole rings of the two tryptophans were perpendicular to each other and their position is consistent with binding n and n+2 xylose residues in the 3-fold helix structure of xylan (Figure 1). The conformation of these aromatic residues are very similar to the pair of tryptophans that interact with xylan in the CBM2s in ''Cellulomonas fimi'' Xyn11A <cite>Simpson1999</cite>. Only Xyl 2 and Xyl3 of the bound xylopentaose made direct interactions with the CBM. It was argued that the paucity of polar interactions enabled the CBM to bind to highly decorated xylans. Mutagenesis studies showed that the two surface trypotphans were essential for xylan recognition. Mutation of the polar residues that had a direct or indirect interaction with xylans or xylopentaose reduced affinity by 100- and 10-fold, respectively <cite>Pell2003</cite>.

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 == Ligand specificities ==
-The three family 15 CBMs (CBM15s) are all derived from the ''Cellvibrio'' bacterial genus. The one fully characterized CBM15 from ''Cellvibrio japonicus'' Xyl10C <cite>Szabo2001</cite> bound to different forms of xylan with a preference for oat spelt xylan (''K''<sub>A</sub> of ~1.4 x 10<sup>4</sup> M<sup>-1</sup>). The CBM also bound to xylooligosacchrides exhibiting affinities for xylohexaose and xylopentaose that were similar to oat spelt xylan, and significantly weaker affinity for xylotetraose and xylotriose.   The protein displayed weak but measurable affinity (KA of ~2 x 10<sup>3</sup> M<sup>-1</sup>) for barley &beta;1,3-&beta;1,4-mixed linked glucan and cellohexaose. The CBM15 did not bind to insoluble xylan or amorphous cellulose. Isothermal titration calorimetry showed that binding to xylan and glucan ligands was driven by enthalpic forces with changes in entropy have a negative impact on affinity <cite>Szabo2001</cite>. The stoichiometry of binding to soluble xylans was consistent with an endo binding mode, demonstrating that the family 15 module is a type B CBM.
+The three family 15 CBMs (CBM15s) are all derived from the ''Cellvibrio'' bacterial genus. The one fully characterized CBM15 module was from ''Cellvibrio japonicus'' Xyl10C <cite>Szabo2001</cite> bound to different forms of xylan with a preference for oat spelt xylan (''K''<sub>A</sub> of ~1.4 x 10<sup>4</sup> M<sup>-1</sup>). The CBM also bound to xylooligosacchrides exhibiting affinities for xylohexaose and xylopentaose that were similar to oat spelt xylan, and significantly weaker affinity for xylotetraose and xylotriose.   The protein displayed weak but measurable affinity (KA of ~2 x 10<sup>3</sup> M<sup>-1</sup>) for barley &beta;1,3-&beta;1,4-mixed linked glucan and cellohexaose. The CBM15 module did not bind to insoluble xylan or amorphous cellulose. Isothermal titration calorimetry showed that binding to xylan and glucan ligands was driven by enthalpic forces with changes in entropy have a negative impact on affinity <cite>Szabo2001</cite>. The stoichiometry of binding to soluble xylans was consistent with an endo binding mode, demonstrating that the family 15 module is a type B CBM.
 == Structural Features ==

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 == Structural Features ==
-[[File:CBM15structure.png|thumb|300px|right|'''Figure 1.'''  The fold of the CBM15 in ''C. japonicus'' Xyn10C (see [{{PDBlink}}1GNY PDB ID 1GNY]) highlighting the two perpendicular tryptophans bound to xylose residues n and n+2 in the 3-fold helical structure of xylan.]]
+[[
-CBM15s comprise ~150 amino acids. The crystal structure of the protein module from the ''C. japonicus'' GH10 xylanase Xyn10C was determined in complex with xylohexaose <cite>Szabo2001</cite>. The structure of CBM15 forms a classic &beta;-jelly roll, predominantly consisting of five major anti-parallel &beta;-strands on the two faces CBM15 contains a deep cleft that runs along the concave face of the &beta;-sheet, 20–25 Å long, which forms the binding site for the target ligands. The protein was crystallized in the presence of xylohexaose, and the structure reveals five well-ordered xylose rings (defined as Xyl1 to Xyl5 from the reducing to non-reducing end). Two solvent-exposed tryptophan residues, Trp176 and Trp181, lie in the binding groove and make hydrophobic stacking interactions with Xyl2 and Xyl4, respectively.  The indole rings of the two tryptophans were perpendicular to each other and their position is consistent with binding n and n+2 xylose residues in the 3-fold helix structure of xylan (Figure 1). The conformation of these aromatic residues are very similar to the pair of tryptophans that interact with xylan in the CBM2s in ''Cellulomonas fimi'' Xyn11A <cite>Simpson1999</cite>. Only Xyl 2 and Xyl3 of the bound xylopentaose made direct interactions with the CBM. It was argued that the paucity of polar interactions enabled the CBM to bind to highly decorated xylans. Mutagenesis studies showed that the two surface trypotphans were essential for xylan recognition. Mutation of the polar residues that had a direct or indirect interaction with xylans or xylopentaose reduced affinity by 100- and 10-fold, respectively <cite>Pell2003</cite>.
 == Functionalities ==