Glycoside Hydrolase Family 112 - Revision history

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

2021-12-18T21:15:22Z

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

Shinya Fushinobu: /* Three-dimensional structures */

2011-09-02T11:30:09Z

Three-dimensional structures

Shinya Fushinobu: /* Three-dimensional structures */

2011-06-01T04:44:39Z

Three-dimensional structures

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

2011-05-27T11:57:03Z

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

Shinya Fushinobu at 09:20, 13 May 2011

2011-05-13T09:20:25Z

Harry Brumer: updated CAZy DB link

2011-05-09T13:26:53Z

updated CAZy DB link

Masafumi Hidaka at 00:48, 26 November 2009

2009-11-26T00:48:02Z

Harry Brumer at 14:18, 8 November 2009

2009-11-08T14:18:30Z

Spencer Williams: /* Kinetics and Mechanism */

2009-09-29T09:44:56Z

Kinetics and Mechanism

Spencer Williams at 09:41, 29 September 2009

2009-09-29T09:41:54Z

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

@@ Line 35: / Line 35: @@
 == Three-dimensional structures ==
 [[Image:GLNBPmov.gif|'''Figure 1:''' Movement of the catalytic TIM barrel domain induced by substrate binding. <span style="color:#0000ff"> The TIM barrel domain is in blue</span>, <span style="color:#00cc00"> an IG-like domain is in green </span>, <span style="color:#999900"> an &alpha;/&beta; domain is in yellow </span> and <span style="color:#ff0000"> a C-terminal domain is in red </span>.|frame|right]]
-The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [PDB ID [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>Hidaka2009</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding ('''Figure 1''').
+The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>Hidaka2009</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding ('''Figure 1''').
 == Family Firsts ==

@@ Line 34: / Line 34: @@
 == Three-dimensional structures ==
-[[Image:GLNBPmov.gif|'''Figure 1:''' Movement of the catalytic TIM barrel domain induced by substrate binding. <span style="color:#0000ff"> The TIM barrel domain is in blue</span>, <span style="color:#00cc00"> an IG-like domain is in green </span>, <span style="color:#999900"> an &alpha;/&beta; domain is in yellow </span> and <span style="color:#ff0000"> a C-terminal domain is in green </span>.|frame|right]]
+[[Image:GLNBPmov.gif|'''Figure 1:''' Movement of the catalytic TIM barrel domain induced by substrate binding. <span style="color:#0000ff"> The TIM barrel domain is in blue</span>, <span style="color:#00cc00"> an IG-like domain is in green </span>, <span style="color:#999900"> an &alpha;/&beta; domain is in yellow </span> and <span style="color:#ff0000"> a C-terminal domain is in red </span>.|frame|right]]
 The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [PDB ID [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>Hidaka2009</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding ('''Figure 1''').

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: [[User:Motomitsu Kitaoka|Motomitsu Kitaoka]]
+* [[Author]]: ^^^Motomitsu Kitaoka^^^
-* [[Responsible Curator]]:  [[User:ShinyaFushinobu|Shinya Fushinobu]]
+* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
 ----
@@ Line 25: / Line 25: @@
 == Substrate specificities ==
-This family of [[glycoside hydrolases]] contains [[phosphorylases]]; beta-galactoside phosphorylase, &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase (EC [{{EClink}}2.4.1.211 2.4.1.211]) <cite>REF1</cite>  and &beta;-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) <cite>REF2</cite>. The former enzymes are subcategorized into galacto-''N''-biose phosphorylase, (GNBP) <cite>REF3</cite>, lacto-''N''-biose I phosphorylase (LNBP) <cite>REF4</cite>, and galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) <cite>REF1,REF4,REF5</cite> based on the substrate preference on galacto-''N''-biose (GNB, Gal-&beta;1,3-GalNAc) and lacto-''N''-biose I (LNB, Gal-&beta;1,3-GlcNAc) <cite>REF4</cite>.
+This family of [[glycoside hydrolases]] contains [[phosphorylases]]; beta-galactoside phosphorylase, &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase (EC [{{EClink}}2.4.1.211 2.4.1.211]) <cite>DerensyDron1999</cite>  and &beta;-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) <cite>Nakajima2009</cite>. The former enzymes are subcategorized into galacto-''N''-biose phosphorylase, (GNBP) <cite>NakajimaAMB2008</cite>, lacto-''N''-biose I phosphorylase (LNBP) <cite>NakajimaAEM2008</cite>, and galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) <cite>DerensyDron1999 NakajimaAEM2008 Kitaoka2005</cite> based on the substrate preference on galacto-''N''-biose (GNB, Gal-&beta;1,3-GalNAc) and lacto-''N''-biose I (LNB, Gal-&beta;1,3-GlcNAc) <cite>NakajimaAEM2008</cite>.
 == Kinetics and Mechanism ==
-Phosphorolysis by GH112 enzymes proceeds with inversion of anomeric configuration, as first shown by Derensy-Dron et al. <cite>REF1</cite> on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'', i.e. LNB + Pi &harr; &alpha;-galactose 1-phosphate + GlcNAc. Considering the topology of the active site structure, the reaction mechanism for [[inverting]] phosphorylase is proposed to be similar to that for [[inverting]] glycoside hydrolases. With the aid of general acid residue, the enzymatic phosphorolysis occurs through direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue in the [[Glycoside Hydrolases#Inverting glycoside hydrolases | inverting glycoside hydrolase]] reaction.
+Phosphorolysis by GH112 enzymes proceeds with inversion of anomeric configuration, as first shown by Derensy-Dron et al. <cite>DerensyDron1999</cite> on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'', i.e. LNB + Pi &harr; &alpha;-galactose 1-phosphate + GlcNAc. Considering the topology of the active site structure, the reaction mechanism for [[inverting]] phosphorylase is proposed to be similar to that for [[inverting]] glycoside hydrolases. With the aid of general acid residue, the enzymatic phosphorolysis occurs through direct nucleophilic attack by phosphate on the anomeric C-1 carbon, instead of the water molecule activated by a general base residue in the [[Glycoside Hydrolases#Inverting glycoside hydrolases | inverting glycoside hydrolase]] reaction.
 == Catalytic Residues ==
-The [[general acid]] residue was firstly estimated by mutational analysis on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF6</cite>.
+The [[general acid]] residue was firstly estimated by mutational analysis on &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Nishimoto2007</cite>.
 == Three-dimensional structures ==
 [[Image:GLNBPmov.gif|'''Figure 1:''' Movement of the catalytic TIM barrel domain induced by substrate binding. <span style="color:#0000ff"> The TIM barrel domain is in blue</span>, <span style="color:#00cc00"> an IG-like domain is in green </span>, <span style="color:#999900"> an &alpha;/&beta; domain is in yellow </span> and <span style="color:#ff0000"> a C-terminal domain is in green </span>.|frame|right]]
-The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [PDB ID [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>REF7</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding ('''Figure 1''').
+The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [PDB ID [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>Hidaka2009</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding ('''Figure 1''').
 == Family Firsts ==
-;First sterochemistry determination: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'' <cite>REF1</cite>.
+;First sterochemistry determination: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium bifidum'' <cite>DerensyDron1999</cite>.
-;First sequence identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF5</cite>.
+;First sequence identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Kitaoka2005</cite>.
-;First [[general acid]] residue identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF6</cite>.
+;First [[general acid]] residue identification: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Nishimoto2007</cite>.
-;First 3-D structure: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>REF7</cite>.
+;First 3-D structure: &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' <cite>Hidaka2009</cite>.
 == References ==
 <biblio>
-#REF1 pmid=9889079
+#DerensyDron1999 pmid=9889079
-#REF2 pmid=19491100
+#Nakajima2009 pmid=19491100
-#REF3 pmid=18183385
+#NakajimaAMB2008 pmid=18183385
-#REF4 pmid=18723650
+#NakajimaAEM2008 pmid=18723650
-#REF5 pmid=15933016
+#Kitaoka2005 pmid=15933016
-#REF6 pmid=17587697
+#Nishimoto2007 pmid=17587697
-#REF7 pmid=19124470
+#Hidaka2009 pmid=19124470
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH112]]

@@ Line 34: / Line 34: @@
 == Three-dimensional structures ==
-The first solved 3-D structure was &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase from ''Bifidobacterium longum'' (PDB [PDB ID [{{PDBlink}}2zuv 2ZUV] in complex with GlcNAc, ethylene glycol, and nitrate) <cite>REF7</cite>. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a &beta;-galactosidase of [[Glycoside Hydrolase Family 42]], supporting the classification of these phosphorolytic enzymes as one of the GH families. A large conformational change in TIM barrel scaffold was observerd with substrate-binding.
+[[Image:GLNBPmov.gif|'''Figure 1:''' Movement of the catalytic TIM barrel domain induced by substrate binding. <span style="color:#0000ff"> The TIM barrel domain is in blue</span>, <span style="color:#00cc00"> an IG-like domain is in green </span>, <span style="color:#999900"> an &alpha;/&beta; domain is in yellow </span> and <span style="color:#ff0000"> a C-terminal domain is in green </span>.|frame|right]]
 == Family Firsts ==

@@ Line 20: / Line 20: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH112.html
+| colspan="2" |{{CAZyDBlink}}GH112.html
 |}
 </div>

← Older revision		Revision as of 14:18, 8 November 2009
Line 1:		Line 1:
		+	{{CuratorApproved}}
	* [[Author]]: [[User:Motomitsu Kitaoka\|Motomitsu Kitaoka]]		* [[Author]]: [[User:Motomitsu Kitaoka\|Motomitsu Kitaoka]]
	* [[Responsible Curator]]: [[User:ShinyaFushinobu\|Shinya Fushinobu]]		* [[Responsible Curator]]: [[User:ShinyaFushinobu\|Shinya Fushinobu]]

@@ Line 24: / Line 24: @@
 == Substrate specificities ==
-This family of [[glycoside hydrolases]] contains beta-galactoside phosphorolyzing enzymes, &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.211 2.4.1.211]) <cite>REF1</cite>  and &beta;-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) <cite>REF2</cite>. The former enzymes are subcategorized into galacto-''N''-biose phosphorylase, (GNBP) <cite>REF3</cite>, lacto-''N''-biose I phosphorylase (LNBP) <cite>REF4</cite>, and galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) <cite>REF1,REF4,REF5</cite> based on the substrate preference on galacto-''N''-biose (GNB, Gal-&beta;1,3-GalNAc) and lacto-''N''-biose I (LNB, Gal-&beta;1,3-GlcNAc) <cite>REF4</cite>.
+This family of [[glycoside hydrolases]] contains [[phosphorylases]]; beta-galactoside phosphorylase, &beta;-1,3-D-galactosyl-D-hexososamine phosphorylase (EC [http://us.expasy.org/cgi-bin/nicezyme.pl?2.4.1.211 2.4.1.211]) <cite>REF1</cite>  and &beta;-1,4-D-galactosyl-L-rhamnose phosphorylase (EC 2.4.1.-) <cite>REF2</cite>. The former enzymes are subcategorized into galacto-''N''-biose phosphorylase, (GNBP) <cite>REF3</cite>, lacto-''N''-biose I phosphorylase (LNBP) <cite>REF4</cite>, and galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) <cite>REF1,REF4,REF5</cite> based on the substrate preference on galacto-''N''-biose (GNB, Gal-&beta;1,3-GalNAc) and lacto-''N''-biose I (LNB, Gal-&beta;1,3-GlcNAc) <cite>REF4</cite>.
 == Kinetics and Mechanism ==