Glycoside Hydrolase Family 98 - Revision history

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

2021-12-18T21:20:05Z

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

Harry Brumer: updated CAZyDBlink

2012-05-11T16:56:51Z

updated CAZyDBlink

Spencer Williams: /* Catalytic Residues */

2011-06-14T03:17:05Z

Catalytic Residues

Harry Brumer at 14:16, 8 November 2009

2009-11-08T14:16:29Z

Al Boraston at 21:34, 27 October 2009

2009-10-27T21:34:03Z

Al Boraston at 21:33, 27 October 2009

2009-10-27T21:33:14Z

Al Boraston at 21:31, 27 October 2009

2009-10-27T21:31:16Z

Al Boraston at 21:30, 27 October 2009

2009-10-27T21:30:42Z

Spencer Williams at 21:35, 21 October 2009

2009-10-21T21:35:24Z

Spencer Williams at 21:34, 21 October 2009

2009-10-21T21:34:41Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Fathima Shaikh^^^
+* [[Author]]: [[User:Fathima Shaikh|Fathima Shaikh]]
-* [[Responsible Curator]]:  ^^^Al Boraston^^^
+* [[Responsible Curator]]:  [[User:Al Boraston|Al Boraston]]
 ----

@@ Line 21: / Line 21: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH98.html
+| colspan="2" |{{CAZyDBlink}}GH98.html
 |}
 </div>

@@ Line 34: / Line 34: @@
 == Catalytic Residues ==
-The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide.  Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.
+The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate dinitrophenyl A-trisaccharide.  Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the p''K''<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.
 == Three-dimensional structures ==

@@ Line 1: / Line 1: @@
-<!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption -->
+{{CuratorApproved}}
 * [[Author]]: ^^^Fathima Shaikh^^^
 * [[Responsible Curator]]:  ^^^Al Boraston^^^

@@ Line 1: / Line 1: @@
 <!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption -->
 * [[Author]]: ^^^Fathima Shaikh^^^
 * [[Responsible Curator]]:  ^^^Al Boraston^^^

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(β1-4)glcNAc] in the AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>.
+The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(β1-4)glcNAc] in the AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. These enzymes are capable of processing these glycans when presented on cell surfaces thus destroying the antigens <cite>Ashida2005 Higgins2009</cite>.
 == Kinetics and Mechanism ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of ABO blood group A and B trisaccharides from glycoconjugates <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. The presence of an L-fucose residue on the substrate is essential for activity of some members of this family (EABase, Sp4GH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. The crystal structure of Sp3GH98 suggests that the L-fucose residue is not required as a specificity determinant in this enzyme <cite>Higgins2009</cite>.
+The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(b1-4)glcNAc] inthe AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>.
 == Kinetics and Mechanism ==
@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub>8</sub> barrel in the catalytic domain <cite>Higgins2009</cite>
+The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub>8</sub> barrel in the catalytic domain with an adjoining β-sandwich domain that contributes to the architecture of the active site and helps define the respective specificities of the enzymes <cite>Higgins2009</cite>
 == Family Firsts ==

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-The [[catalytic base]], an aspartate and glutamate diad, and the [[catalytic acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide.  Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.
+The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide.  Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.
 == Three-dimensional structures ==
@@ Line 43: / Line 43: @@
 ;First sterochemistry determination
 :''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.
-;First [[catalytic base]] identification
+;First [[general base]] identification
 :''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.
 :''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.
-;First [[catalytic acid]] identification
+;First [[general acid]] identification
 :''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.
 :''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.