Glycoside Hydrolase Family 54 - Revision history

Shinya Fushinobu at 09:38, 13 May 2014

2014-05-13T09:38:41Z

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

2011-05-27T11:22:06Z

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

Shinya Fushinobu at 01:24, 25 November 2009

2009-11-25T01:24:22Z

Harry Brumer at 14:10, 8 November 2009

2009-11-08T14:10:45Z

Shinya Fushinobu at 02:55, 28 October 2009

2009-10-28T02:55:14Z

Shinya Fushinobu at 09:04, 27 October 2009

2009-10-27T09:04:54Z

Shinya Fushinobu at 08:36, 27 October 2009

2009-10-27T08:36:04Z

Spencer Williams: /* Family Firsts */

2009-09-30T12:08:52Z

Family Firsts

Spencer Williams: /* Kinetics and Mechanism */

2009-09-30T10:16:40Z

Kinetics and Mechanism

Spencer Williams: /* Family Firsts */

2009-09-30T10:16:03Z

Family Firsts

@@ Line 38: / Line 38: @@
 == Carbohydrate-Binding Module ==
-Most of the members in GH54 have [[Carbohydrate-Binding Module Family 42]] of approximately 160 residues at the C-terminus of GH54 catalytic domains. This module was firstly found as a xylan binding domain <cite>Nogawa1999</cite>, and binding to arabinofuranose (present in arabinoxylan) has been subsequently demonstrated <cite>Miyanaga2006</cite>.
+Most of the members in GH54 have [[CBM42]] of approximately 160 residues at the C-terminus of GH54 catalytic domains. This module was firstly found as a xylan binding domain <cite>Nogawa1999</cite>, and binding to arabinofuranose (present in arabinoxylan) has been subsequently demonstrated <cite>Miyanaga2006</cite>.
 == Family Firsts ==

@@ Line 20: / Line 20: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH54.html
+| colspan="2" |{{CAZyDBlink}}GH54.html
 |}
 </div>
@@ Line 28: / Line 28: @@
 == Kinetics and Mechanism ==
-[[Glycoside hydrolases]] of family 54 are [[retaining]] enzymes. In 1996, many &alpha;-L-arabinofuranosidases from fungi, including GH54 arabinofuranosidase B from ''Aspergillus niger'', were shown to use a [[retaining]] mechanism by <sup>1</sup>H NMR analysis using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and by measurement of glycosyl transfer reactions to methanol <cite>REF1</cite>. In the 1980's, two &alpha;-L-arabinofuranosidases (AF I and AF III) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=38457 ''Monilinia fructigena''] were shown to be [[retaining]] enzymes by various methods including suicide inactivation with <sup>3</sup>H-labelled 1-&alpha;-L-arabinofuranosylmethyl-3-''p''-nitrophenyltriazene as well as measurement of glycosyl transfer reactions using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and methanol <cite>REF2 REF3</cite>, but the genes for these enzymes are not cloned yet. If either AF I or AF III belongs to GH54, one of these studies represents the first stereochemistry determination of this family.
+[[Glycoside hydrolases]] of family 54 are [[retaining]] enzymes. In 1996, many &alpha;-L-arabinofuranosidases from fungi, including GH54 arabinofuranosidase B from ''Aspergillus niger'', were shown to use a [[retaining]] mechanism by <sup>1</sup>H NMR analysis using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and by measurement of glycosyl transfer reactions to methanol <cite>Pitson1996</cite>. In the 1980's, two &alpha;-L-arabinofuranosidases (AF I and AF III) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=38457 ''Monilinia fructigena''] were shown to be [[retaining]] enzymes by various methods including suicide inactivation with <sup>3</sup>H-labelled 1-&alpha;-L-arabinofuranosylmethyl-3-''p''-nitrophenyltriazene as well as measurement of glycosyl transfer reactions using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and methanol <cite>Fielding1981 Kelly1987</cite>, but the genes for these enzymes are not cloned yet. If either AF I or AF III belongs to GH54, one of these studies represents the first stereochemistry determination of this family.
 == Catalytic Residues ==
-The catalytic residues were firstly estimated by superimposing the active site structure of &alpha;-L-arabinofuranosidase B (AkAbfB) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] with a [[Glycoside Hydrolase Family 51]] enzyme, &alpha;-L-arabinofuranosidase A from ''Geobacillus stearothermophilus'' T-6. Based on the relative positions with an arabinose molecule, Glu221 and Asp297 were estimated as the [[catalytic nucleophile]] and the [[general acid/base]], respectively. E221A mutant of this enzyme showed no detectable activity, and E297A mutant showed 10<sup>-3</sup>-fold activity of wild type <cite>REF4</cite>.<br>
+The catalytic residues were firstly estimated by superimposing the active site structure of &alpha;-L-arabinofuranosidase B (AkAbfB) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] with a [[Glycoside Hydrolase Family 51]] enzyme, &alpha;-L-arabinofuranosidase A from ''Geobacillus stearothermophilus'' T-6. Based on the relative positions with an arabinose molecule, Glu221 and Asp297 were estimated as the [[catalytic nucleophile]] and the [[general acid/base]], respectively. E221A mutant of this enzyme showed no detectable activity, and E297A mutant showed 10<sup>-3</sup>-fold activity of wild type <cite>Miyanaga2004</cite>.<br>
-Kinetic studies using mutant enzymes of &alpha;-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=97093 ''Trichoderma koningii''] G-39 confirmed this assignment <cite>REF8</cite>.
+Kinetic studies using mutant enzymes of &alpha;-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=97093 ''Trichoderma koningii''] G-39 confirmed this assignment <cite>Wan2007</cite>.
 == Three-dimensional structures ==
-The first solved 3-D structure was &alpha;-L-arabinofuranosidase B (AkAbfB) from ''Aspergillus kawachii'' IFO 4308 (PDB ID [{{PDBlink}}1wd4 1wd4] in complex with arabinose) in 2004 <cite>REF4</cite>. This family has a &beta;-jelly roll fold that is slightly similar to [http://www.cazy.org/fam/acc_GH.html#table Clan GH-B]. The position of the [[catalytic nucleophile]] is superimposable with Clan GH-B, whereas the [[general acid/base]] is not.
+The first solved 3-D structure was &alpha;-L-arabinofuranosidase B (AkAbfB) from ''Aspergillus kawachii'' IFO 4308 (PDB ID [{{PDBlink}}1wd4 1wd4] in complex with arabinose) in 2004 <cite>Miyanaga2004</cite>. This family has a &beta;-jelly roll fold that is slightly similar to [http://www.cazy.org/fam/acc_GH.html#table Clan GH-B]. The position of the [[catalytic nucleophile]] is superimposable with Clan GH-B, whereas the [[general acid/base]] is not.
 == Carbohydrate-Binding Module ==
-Most of the members in GH54 have [[Carbohydrate-Binding Module Family 42]] of approximately 160 residues at the C-terminus of GH54 catalytic domains. This module was firstly found as a xylan binding domain <cite>REF5</cite>, and binding to arabinofuranose (present in arabinoxylan) has been subsequently demonstrated <cite>REF6</cite>.
+Most of the members in GH54 have [[Carbohydrate-Binding Module Family 42]] of approximately 160 residues at the C-terminus of GH54 catalytic domains. This module was firstly found as a xylan binding domain <cite>Nogawa1999</cite>, and binding to arabinofuranose (present in arabinoxylan) has been subsequently demonstrated <cite>Miyanaga2006</cite>.
 == Family Firsts ==
-;First sterochemistry determination: Probably ABF B from ''Aspergillus niger'' and other fungal enzymes by <sup>1</sup>H NMR spectroscopy and glycosyl transfer reaction measurements <cite>REF1</cite>. See [[#Kinetics and Mechanism|kinetics and mechanism]].
+;First sterochemistry determination: Probably ABF B from ''Aspergillus niger'' and other fungal enzymes by <sup>1</sup>H NMR spectroscopy and glycosyl transfer reaction measurements <cite>Pitson1996</cite>. See [[#Kinetics and Mechanism|kinetics and mechanism]].
-;First gene cloning: &alpha;-L-Arabinofuranosidase (ABF B) from ''Aspergillus niger'' ([http://www.uniprot.org/uniprot/P42255 Uniprot P42255]) <cite>REF7</cite>.
+;First gene cloning: &alpha;-L-Arabinofuranosidase (ABF B) from ''Aspergillus niger'' ([http://www.uniprot.org/uniprot/P42255 Uniprot P42255]) <cite>Flipphi1993</cite>.
 ;First [[catalytic nucleophile]] identification: AkAbfB from ''Aspergillus kawachii'' by structural comparison and mutation.
 ;First [[general acid/base]] residue identification: AkAbfB from ''Aspergillus kawachii'' by structural comparison and mutation.
-;First 3-D structure: AkAbfB from ''Aspergillus kawachii'' by X-ray crystallography <cite>REF4</cite>.
+;First 3-D structure: AkAbfB from ''Aspergillus kawachii'' by X-ray crystallography <cite>Miyanaga2004</cite>.
 == References ==
 <biblio>
-#REF1 pmid=8946944
+#Pitson1996 pmid=8946944
-#REF2 Fielding, A. H., Sinnott, M. L., Kelly, M. A., and Widdows, D. (1981) ''Product stereochemistry and some inhibitors of the alpha-arabinofuranosidases of Monilinia fructigena.'' J. Chem. Soc., Perkin Trans. 1, 1013-1014. doi:10.1039/P19810001013.
+#Fielding1981 Fielding, A. H., Sinnott, M. L., Kelly, M. A., and Widdows, D. (1981) ''Product stereochemistry and some inhibitors of the alpha-arabinofuranosidases of Monilinia fructigena.'' J. Chem. Soc., Perkin Trans. 1, 1013-1014. doi:10.1039/P19810001013.
-#REF3 pmid=3663195
+#Kelly1987 pmid=3663195
-#REF4 pmid=15292273
+#Miyanaga2004 pmid=15292273
-#REF5 pmid=10473402
+#Nogawa1999 pmid=10473402
-#REF6 pmid=16846393
+#Miyanaga2006 pmid=16846393
-#REF7 pmid=8299175
+#Flipphi1993 pmid=8299175
-#REF8 pmid=17002602
+#Wan2007 pmid=17002602
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH054]]

@@ Line 25: / Line 25: @@
 == Substrate specificities ==
-This family of [[glycoside hydrolases]] contains &alpha;-L-arabinofuranosidase (EC[http://us.expasy.org/cgi-bin/nicezyme.pl?3.2.1.55 3.2.1.55]) and &beta;-xylosidase (EC[http://us.expasy.org/cgi-bin/nicezyme.pl?3.2.1.37 3.2.1.37]). Most of the family members have eukaryotic (fungal) origin. Several homologous genes are found from Bacterial genomes, but none of their gene products are characterized.
+This family of [[glycoside hydrolases]] contains &alpha;-L-arabinofuranosidase (EC [{{EClink}}3.2.1.55 3.2.1.55]) and &beta;-xylosidase (EC [{{EClink}}3.2.1.37 3.2.1.37]). Most of the family members have eukaryotic (fungal) origin. Several homologous genes are found from Bacterial genomes, but none of their gene products are characterized.
 == Kinetics and Mechanism ==
@@ Line 35: / Line 35: @@
 == Three-dimensional structures ==
-The first solved 3-D structure was &alpha;-L-arabinofuranosidase B (AkAbfB) from ''Aspergillus kawachii'' IFO 4308 ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1WD4 PDB 1wd4] in complex with arabinose) in 2004 <cite>REF4</cite>. This family has a &beta;-jelly roll fold that is slightly similar to [http://www.cazy.org/fam/acc_GH.html#table Clan GH-B]. The position of the [[catalytic nucleophile]] is superimposable with Clan GH-B, whereas the [[general acid/base]] is not.
+The first solved 3-D structure was &alpha;-L-arabinofuranosidase B (AkAbfB) from ''Aspergillus kawachii'' IFO 4308 (PDB ID [{{PDBlink}}1wd4 1wd4] in complex with arabinose) in 2004 <cite>REF4</cite>. This family has a &beta;-jelly roll fold that is slightly similar to [http://www.cazy.org/fam/acc_GH.html#table Clan GH-B]. The position of the [[catalytic nucleophile]] is superimposable with Clan GH-B, whereas the [[general acid/base]] is not.
 == Carbohydrate-Binding Module ==

← Older revision		Revision as of 14:10, 8 November 2009
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		+	{{CuratorApproved}}
	* [[Author]]: [[User:ShinyaFushinobu\|Shinya Fushinobu]]		* [[Author]]: [[User:ShinyaFushinobu\|Shinya Fushinobu]]
	* [[Responsible Curator]]: [[User:ShinyaFushinobu\|Shinya Fushinobu]]		* [[Responsible Curator]]: [[User:ShinyaFushinobu\|Shinya Fushinobu]]

@@ Line 27: / Line 27: @@
 == Kinetics and Mechanism ==
-[[Glycoside hydrolases]] of family 54 are [[retaining]] enzymes. In 1996, many &alpha;-L-arabinofuranosidases from fungi, including GH54 arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5061 ''Aspergillus niger''], were shown to use a [[retaining]] mechanism by <sup>1</sup>H NMR analysis using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and by measurement of glycosyl transfer reactions to methanol <cite>REF1</cite>. In the 1980's, two &alpha;-L-arabinofuranosidases (AF I and AF III) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=38457 ''Monilinia fructigena''] were shown to be [[retaining]] enzymes by various methods including suicide inactivation with <sup>3</sup>H-labelled 1-&alpha;-L-arabinofuranosylmethyl-3-''p''-nitrophenyltriazene as well as measurement of glycosyl transfer reactions using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and methanol <cite>REF2</cite><cite>REF3</cite>, but the genes for these enzymes are not cloned yet. If either AF I or AF III belongs to GH54, one of these studies represents the first stereochemistry determination of this family.
+[[Glycoside hydrolases]] of family 54 are [[retaining]] enzymes. In 1996, many &alpha;-L-arabinofuranosidases from fungi, including GH54 arabinofuranosidase B from ''Aspergillus niger'', were shown to use a [[retaining]] mechanism by <sup>1</sup>H NMR analysis using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and by measurement of glycosyl transfer reactions to methanol <cite>REF1</cite>. In the 1980's, two &alpha;-L-arabinofuranosidases (AF I and AF III) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=38457 ''Monilinia fructigena''] were shown to be [[retaining]] enzymes by various methods including suicide inactivation with <sup>3</sup>H-labelled 1-&alpha;-L-arabinofuranosylmethyl-3-''p''-nitrophenyltriazene as well as measurement of glycosyl transfer reactions using ''p''-nitrophenyl &alpha;-L-arabinofuranoside and methanol <cite>REF2 REF3</cite>, but the genes for these enzymes are not cloned yet. If either AF I or AF III belongs to GH54, one of these studies represents the first stereochemistry determination of this family.
 == Catalytic Residues ==
-The catalytic residues were firstly estimated by superimposing the active site structure of &alpha;-L-arabinofuranosidase B (AkAbfB) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] with a [[Glycoside Hydrolase Family 51]] enzyme, &alpha;-L-arabinofuranosidase A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1422 ''Geobacillus stearothermophilus''] T-6. Based on the relative positions with an arabinose molecule, Glu221 and Asp297 were estimated as the [[catalytic nucleophile]] and the [[general acid/base]], respectively. E221A mutant of this enzyme showed no detectable activity, and E297A mutant showed 10<sup>-3</sup>-fold activity of wild type <cite>REF4</cite>.<br>
+The catalytic residues were firstly estimated by superimposing the active site structure of &alpha;-L-arabinofuranosidase B (AkAbfB) from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] with a [[Glycoside Hydrolase Family 51]] enzyme, &alpha;-L-arabinofuranosidase A from ''Geobacillus stearothermophilus'' T-6. Based on the relative positions with an arabinose molecule, Glu221 and Asp297 were estimated as the [[catalytic nucleophile]] and the [[general acid/base]], respectively. E221A mutant of this enzyme showed no detectable activity, and E297A mutant showed 10<sup>-3</sup>-fold activity of wild type <cite>REF4</cite>.<br>
 Kinetic studies using mutant enzymes of &alpha;-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=97093 ''Trichoderma koningii''] G-39 confirmed this assignment <cite>REF8</cite>.