Glycoside Hydrolase Family 79 - Revision history

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

2021-12-18T21:17:38Z

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

Spencer Williams at 01:26, 26 November 2012

2012-11-26T01:26:43Z

Harry Brumer: updated EC link

2012-11-08T16:14:56Z

updated EC link

Zui Fujimoto: /* References */

2012-11-08T06:53:10Z

References

Zui Fujimoto: /* References */

2012-11-08T06:51:51Z

References

Hitomi Ichinose at 14:08, 21 March 2012

2012-03-21T14:08:01Z

Harry Brumer at 01:15, 10 March 2012

2012-03-10T01:15:21Z

Harry Brumer: /* Three-dimensional structures */

2012-03-10T00:48:04Z

Three-dimensional structures

Harry Brumer: /* Three-dimensional structures */

2012-03-10T00:45:56Z

Three-dimensional structures

Harry Brumer: /* Catalytic Residues */

2012-03-10T00:44:12Z

Catalytic Residues

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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]]: ^^^Hitomi Ichinose^^^ and ^^^Satoshi Kaneko^^^
+* [[Author]]: [[User:Hitomi Ichinose|Hitomi Ichinose]] and [[User:Satoshi Kaneko|Satoshi Kaneko]]
-* [[Responsible Curator]]:  ^^^Satoshi Kaneko^^^
+* [[Responsible Curator]]:  [[User:Satoshi Kaneko|Satoshi Kaneko]]
 ----

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 == Substrate specificities ==
-Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (EC [{{EClink}}3.2.1.31 3.2.1.31]) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (EC 3.2.1.-) <cite>Kuroyama2001</cite>, baicalin β-glucuronidase (EC [{{EClink}}3.2.1.167 3.2.1.167]) <cite> Sasaki2000 </cite>, heparanase (EC [{{EClink}}3.2.1.166 3.2.1.166]) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (EC 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
+Family GH79 [[glycoside hydrolases]] are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (EC [{{EClink}}3.2.1.31 3.2.1.31]) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (EC 3.2.1.-) <cite>Kuroyama2001</cite>, baicalin β-glucuronidase (EC [{{EClink}}3.2.1.167 3.2.1.167]) <cite> Sasaki2000 </cite>, heparanase (EC [{{EClink}}3.2.1.166 3.2.1.166]) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (EC 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
-Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite>. Heparanase is an endo-β-glucuronidase that degrades the heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').
+Some GH79 β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite>. Heparanase is an endo-β-glucuronidase that degrades the heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').
 == Kinetics and Mechanism ==
-GH79 β-glucuronidases are retaining enzymes, as first demonstrated by proton-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.
+GH79 β-glucuronidases are [[retaining]] enzymes, as first demonstrated by <sup>1</sup>-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.
 == Catalytic Residues ==
-The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 (acid/base) and Glu287 (nucleophile) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and site-directed mutagenesis studies <cite> Michikawa2012 </cite>.
+The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 ([[general acid/base]]) and Glu287 ([[catalytic nucleophile]]) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and site-directed mutagenesis studies <cite> Michikawa2012 </cite>.
 == Three-dimensional structures ==
-The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.
+The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub> TIM-barrel fold, as found for all members of [[clan]] GH-A.
 == Family Firsts ==
-;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by 1H-NMR <cite> Michikawa2012 </cite>.
+;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by <sup>1</sup>H-NMR <cite> Michikawa2012 </cite>.
-;First catalytic nucleophile identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.
+;First [[catalytic nucleophile]] identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.
-;First general acid/base residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.
+;First [[general acid/base]] residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.
 ;First 3-D structure: ''A. capsulatum'' β-glucuronidase (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>.

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 == Substrate specificities ==
-Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (EC [{{EClink}}3.2.1.31 3.2.1.31]) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (EC 3.2.1.-) <cite>Kuroyama2001</cite>, baicalin β-glucuronidase (EC [{{EClink}}3.2.1.167 3.2.1.167]) <cite> Sasaki2000 </cite>, heparanase (EC 3.2.1.166) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (EC 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
+Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (EC [{{EClink}}3.2.1.31 3.2.1.31]) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (EC 3.2.1.-) <cite>Kuroyama2001</cite>, baicalin β-glucuronidase (EC [{{EClink}}3.2.1.167 3.2.1.167]) <cite> Sasaki2000 </cite>, heparanase (EC [{{EClink}}3.2.1.166 3.2.1.166]) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (EC 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
 Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite>. Heparanase is an endo-β-glucuronidase that degrades the heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').

@@ Line 54: / Line 54: @@
 #Konishi2008 pmid=18377882
 #Sasaki2000 pmid=10858442
-#Michikawa2012 pmid=22878205
+#Michikawa2012 pmid=22367201
 #Vlodavsky1999 pmid=10395325
 #Toyoshima1999 pmid=10446189

@@ Line 54: / Line 54: @@
 #Konishi2008 pmid=18377882
 #Sasaki2000 pmid=10858442
-#Michikawa2012 Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers S, Fujimoto Z, Kaneko S. ''Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from Acidobacterium capsulatum.'' J. Biol. Chem. in press.  //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1074/jbc.M112.346288                                     DOI:10.1074/jbc.M112.346288] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22367201 PMID: 22367201]
+#Michikawa2012 pmid=22878205
 #Vlodavsky1999 pmid=10395325
 #Toyoshima1999 pmid=10446189

@@ Line 40: / Line 40: @@
 == Three-dimensional structures ==
-The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.
+The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 (PDB ID [{{PDBlink}}3VO0 3VO0] <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.
 == Family Firsts ==