Glycoside Hydrolase Family 94 - Revision history

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

2021-12-18T21:19:20Z

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

Harry Brumer: /* Substrate specificities */

2011-05-27T11:35:01Z

Substrate specificities

Harry Brumer: updated reference identifiers to standard AuthorYear format to make future edting easier

2011-05-27T11:34:52Z

updated reference identifiers to standard AuthorYear format to make future edting easier

Masafumi Hidaka at 02:17, 25 November 2009

2009-11-25T02:17:35Z

Masafumi Hidaka at 02:08, 25 November 2009

2009-11-25T02:08:42Z

Harry Brumer at 14:15, 8 November 2009

2009-11-08T14:15:28Z

Spencer Williams at 10:18, 30 September 2009

2009-09-30T10:18:02Z

Masafumi Hidaka: /* Three-dimensional structures */

2009-09-06T04:46:17Z

Three-dimensional structures

Spencer Williams at 04:42, 1 September 2009

2009-09-01T04:42:33Z

Motomitsu Kitaoka: /* Substrate specificities */

2009-08-06T01:59:17Z

Substrate specificities

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Masafumi Hidaka^^^
+* [[Author]]: [[User:Masafumi Hidaka|Masafumi Hidaka]]
-* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
+* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 ----

@@ Line 26: / Line 26: @@
 == Substrate specificities ==
 This family of [[glycoside hydrolase]]s exclusively contains [[phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [{{EClink}}2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [{{EClink}}2.4.1.49 2.4.1.49]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a [[glycosyltransferase]] domain from [[Glycosyltransferase Family 84]] <cite>Ciocchini2007</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.
 GH94 enzymes were initially classified in [[Glycosyltransferase Family 36]] because none of them show hydrolytic activity. However because of the evolutionary, structural and mechanistic relatedness with clan GH-L glycoside hydrolases, the family was re-assigned to family GH94 <cite>Hidaka2004</cite>.

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: [[User:Masafumi_Hidaka|Masafumi Hidaka]]
+* [[Author]]: ^^^Masafumi Hidaka^^^
-* [[Responsible Curator]]:  [[User:Shinya_Fushinobu|Shinya Fushinobu]]
+* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
 ----
@@ Line 20: / Line 20: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH94.html
+| colspan="2" |{{CAZyDBlink}}GH94.html
 |}
 </div>
 == Substrate specificities ==
-This family of [[glycoside hydrolase]]s exclusively contains [[phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [{{EClink}}2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [{{EClink}}2.4.1.49 2.4.1.49]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a [[glycosyltransferase]] domain from [[Glycosyltransferase Family 84]] <cite>REF7</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.<BR>
+This family of [[glycoside hydrolase]]s exclusively contains [[phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [{{EClink}}2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [{{EClink}}2.4.1.49 2.4.1.49]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a [[glycosyltransferase]] domain from [[Glycosyltransferase Family 84]] <cite>Ciocchini2007</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.
-GH94 enzymes were initially classified in [[Glycosyltransferase Family 36]] because none of them show hydrolytic activity. However because of the evolutionary, structural and mechanistic relatedness with clan GH-L glycoside hydrolases, the family was re-assigned to family GH94 <cite>REF1</cite>.
 == Kinetics and Mechanism ==
-Phosphorolysis by GH94 enzymes proceeds with inversion of anomeric configuration, as first shown by Sih and McBee <cite>REF5</cite> on cellobiose phosphorylase from ''Clostridium thermocellum'', i.e. cellobiose (Glc-&beta;1,4-Glc) + Pi &harr; &alpha;-glucose 1-phosphate + glucose; these are therefore [[inverting]] enzymes. Considering the topology of the active site structure, the reaction mechanism for [[inverting]] phosphorylases is proposed to be similar to that for inverting GHs <cite>REF1</cite>. With the aid of a general acid residue, enzymatic phosphorolysis begins with direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue, as in inverting GH reaction.
+Phosphorolysis by GH94 enzymes proceeds with inversion of anomeric configuration, as first shown by Sih and McBee <cite>Sih1955</cite> on cellobiose phosphorylase from ''Clostridium thermocellum'', i.e. cellobiose (Glc-&beta;1,4-Glc) + Pi &harr; &alpha;-glucose 1-phosphate + glucose; these are therefore [[inverting]] enzymes. Considering the topology of the active site structure, the reaction mechanism for [[inverting]] phosphorylases is proposed to be similar to that for inverting GHs <cite>Hidaka2004</cite>. With the aid of a general acid residue, enzymatic phosphorolysis begins with direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue, as in inverting GH reaction.
 == Catalytic Residues ==
-The [[general acid]] residue was first elucidated by superimposing the active site structure of chitobiose phosphorylase from ''Vibrio proteolyticus'' with a [[Glycoside Hydrolase Family 15]] enzyme, glucoamylase from ''Thermoanaerobacterium thermosaccharolyticum'' <cite>REF1</cite>. Considering the similarities of the active site structure, Asp492 was identified as the general acid residue. D492A/N mutants of this enzyme showed no detectable activity. A general base residue is not required in the reaction catalyzed by glycoside hydrolase-like [[inverting]] phosphorylases.
+The [[general acid]] residue was first elucidated by superimposing the active site structure of chitobiose phosphorylase from ''Vibrio proteolyticus'' with a [[Glycoside Hydrolase Family 15]] enzyme, glucoamylase from ''Thermoanaerobacterium thermosaccharolyticum'' <cite>Hidaka2004</cite>. Considering the similarities of the active site structure, Asp492 was identified as the general acid residue. D492A/N mutants of this enzyme showed no detectable activity. A general base residue is not required in the reaction catalyzed by glycoside hydrolase-like [[inverting]] phosphorylases.
 == Three-dimensional structures ==
 The first solved 3-D structure was chitobiose phosphorylase from ''Vibrio proteolyticus'' (PDB
-[PDB ID [{{PDBlink}}1v7x 1v7x] in complex with GlcNAc and sulfate ) <cite>REF1</cite>. The enzyme has a (&alpha;/&alpha;)<sub>6</sub> barrel fold that is remarkably similar to clan GH-L. The position of the catalytic general acid is superimposable with Clan GH-L. It should be noted that GH94 enzymes act on &beta;-bonds, whereas clan GH-L enzymes ([[Glycoside Hydrolase Family 15]] and [[Glycoside Hydrolase Family 65]]) act on &alpha;-bonds.
+[PDB ID [{{PDBlink}}1v7x 1v7x] in complex with GlcNAc and sulfate ) <cite>Hidaka2004</cite>. The enzyme has a (&alpha;/&alpha;)<sub>6</sub> barrel fold that is remarkably similar to clan GH-L. The position of the catalytic general acid is superimposable with Clan GH-L. It should be noted that GH94 enzymes act on &beta;-bonds, whereas clan GH-L enzymes ([[Glycoside Hydrolase Family 15]] and [[Glycoside Hydrolase Family 65]]) act on &alpha;-bonds.
 == Family Firsts ==
 ;First sterochemistry determination:
-Cellobiose phosphorylase from ''Clostridium thermocellum'' <cite>REF5</cite>
+Cellobiose phosphorylase from ''Clostridium thermocellum'' <cite>Sih1955</cite>
 ;First gene cloning:
-Cellobiose phosphorylase and a cellodextrin phosphorylase from ''Clostridium stercorarium'' <cite>REF6</cite>
+Cellobiose phosphorylase and a cellodextrin phosphorylase from ''Clostridium stercorarium'' <cite>Reichenbecher1997</cite>
 ;First general acid residue identification:
-''Vibrio proteolyticus'' chitobiose phosphorylase by kinetic studies with mutants <cite>REF1</cite>
+''Vibrio proteolyticus'' chitobiose phosphorylase by kinetic studies with mutants <cite>Hidaka2004</cite>
 ;First 3-D structure:
-''Vibrio proteolyticus'' chitobiose phosphorylase <cite>REF1</cite>.
+''Vibrio proteolyticus'' chitobiose phosphorylase <cite>Hidaka2004</cite>.
 == References ==
 <biblio>
-#REF1 pmid=15274915
+#Hidaka2004 pmid=15274915
-#REF5 Sih CJ, and McBee RH. ''A cellobiose phosphorylase in Clostridium thermocellum.'' Proc Montana Acad Sci 1955, 15, 21-22.
+#Sih1955 Sih CJ, and McBee RH. ''A cellobiose phosphorylase in Clostridium thermocellum.'' Proc Montana Acad Sci 1955, 15, 21-22.
-#REF6 pmid=9249035
+#Reichenbecher1997 pmid=9249035
-#REF7 pmid=17921247
+#Ciocchini2007 pmid=17921247
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH094]]

@@ Line 37: / Line 37: @@
 == Three-dimensional structures ==
 The first solved 3-D structure was chitobiose phosphorylase from ''Vibrio proteolyticus'' (PDB
-[http://www.rcsb.org/pdb/explore/explore.do?structureId=1V7X 1V7X] in complex with GlcNAc and sulfate ) <cite>REF1</cite>. The enzyme has a (&alpha;/&alpha;)<sub>6</sub> barrel fold that is remarkably similar to clan GH-L. The position of the catalytic general acid is superimposable with Clan GH-L. It should be noted that GH94 enzymes act on &beta;-bonds, whereas clan GH-L enzymes ([[Glycoside Hydrolase Family 15]] and [[Glycoside Hydrolase Family 65]]) act on &alpha;-bonds.
+[PDB ID [{{PDBlink}}1v7x 1v7x] in complex with GlcNAc and sulfate ) <cite>REF1</cite>. The enzyme has a (&alpha;/&alpha;)<sub>6</sub> barrel fold that is remarkably similar to clan GH-L. The position of the catalytic general acid is superimposable with Clan GH-L. It should be noted that GH94 enzymes act on &beta;-bonds, whereas clan GH-L enzymes ([[Glycoside Hydrolase Family 15]] and [[Glycoside Hydrolase Family 65]]) act on &alpha;-bonds.
 == Family Firsts ==

@@ Line 25: / Line 25: @@
 == Substrate specificities ==
-This family of [[glycoside hydrolase]]s exclusively contains [[phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.49 2.4.1.49]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a [[glycosyltransferase]] domain from [[Glycosyltransferase Family 84]] <cite>REF7</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.<BR>
+This family of [[glycoside hydrolase]]s exclusively contains [[phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [{{EClink}}2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [{{EClink}}2.4.1.49 2.4.1.49]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a [[glycosyltransferase]] domain from [[Glycosyltransferase Family 84]] <cite>REF7</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.<BR>
 GH94 enzymes were initially classified in [[Glycosyltransferase Family 36]] because none of them show hydrolytic activity. However because of the evolutionary, structural and mechanistic relatedness with clan GH-L glycoside hydrolases, the family was re-assigned to family GH94 <cite>REF1</cite>.

← Older revision		Revision as of 14:15, 8 November 2009
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		+	{{CuratorApproved}}
	* [[Author]]: [[User:Masafumi_Hidaka\|Masafumi Hidaka]]		* [[Author]]: [[User:Masafumi_Hidaka\|Masafumi Hidaka]]
	* [[Responsible Curator]]: [[User:Shinya_Fushinobu\|Shinya Fushinobu]]		* [[Responsible Curator]]: [[User:Shinya_Fushinobu\|Shinya Fushinobu]]

@@ Line 24: / Line 24: @@
 == Substrate specificities ==
-This family exclusively contains [[Phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.29 2.4.1.29]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a glycosyltransferase domain from [[GlycosylTransferase Family 84]] <cite>REF7</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.<BR>
+This family exclusively contains [[Phosphorylases]] that cleave &beta;-glycosidic bonds. The substrate specificities found in GH94 are: cellobiose (Glc-&beta;1,4-Glc) phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.20 2.4.1.20]), cellodextrin ((Glc-&beta;1,4-)<sub>n-1</sub>Glc; n &ge; 3) phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.49 2.4.1.49]), and N,N’-diacetyl chitobiose (GlcNAc-&beta;1,4-GlcNAc) phosphorylase. Moreover, a phosphorylase domain belonging to this family is found in cyclic &beta;-1,2-glucan synthase, a modular protein that also contains a glycosyltransferase domain from [[GlycosylTransferase Family 84]] <cite>REF7</cite>. The GH94 domain is thought to phosphorolyze protein-bound &beta;-1,2-glucans synthesized from UDP-glucose by the GT84 domain.<BR>
 GH94 enzymes were initially classified in [[GlycosylTransferase Family 36]] because none of them show hydrolytic activity. However because of the evolutionary, structural and mechanistic relatedness with clan GH-L glycoside hydrolases, the family was re-assigned to family GH94 <cite>REF1</cite>.