Glycoside Hydrolase Family 115 - Revision history

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

2021-12-18T21:16:41Z

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

Karen Eddy at 22:28, 21 June 2012

2012-06-21T22:28:39Z

Karen Eddy at 22:28, 21 June 2012

2012-06-21T22:28:09Z

Karen Eddy at 22:27, 21 June 2012

2012-06-21T22:27:22Z

Spencer Williams at 01:24, 9 June 2011

2011-06-09T01:24:39Z

Spencer Williams at 12:08, 8 June 2011

2011-06-08T12:08:50Z

Spencer Williams at 11:18, 12 May 2011

2011-05-12T11:18:36Z

Harry Brumer: /* References */

2011-05-12T08:40:10Z

References

Harry Brumer at 08:39, 12 May 2011

2011-05-12T08:39:44Z

Harry Brumer: /* Kinetics and Mechanism */

2011-05-12T08:35:57Z

Kinetics and Mechanism

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

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 #Kolenova2010 pmid=20804758
 #Fujimoto2011 pmid=21206027
-#Chong2011 Chong SL, Battaglia E, Coutinho PM, Henrissat B, Tenkanen M, de Vries RP. ''The α-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase family (GH115).'' Appl Microbiol Biotechnol. 2011 May;90(4):1323-1332. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1007/s00253-011-3157-y DOI:10.1007/s00253-011-3157-y] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21442271 PMID: 21442271]
+#Chong2011 pmid=21442271
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH115]]

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 #Ryabova2009 pmid=19344716
 #Kolenova2010 pmid=20804758
-#Fujimoto2011 Fujimoto Z, Ichinose H, Biely P, Kaneko S. ''Crystallization and preliminary crystallographic analysis of the glycoside hydrolase family 115 α-glucuronidase from Streptomyces pristinaespiralis.'' Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jan 1;67(Pt 1):68-71. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1107/S1744309110043721 DOI:10.1107/S1744309110043721] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21206027 PMID: 21206027]
+#Fujimoto2011 pmid=21206027
 #Chong2011 Chong SL, Battaglia E, Coutinho PM, Henrissat B, Tenkanen M, de Vries RP. ''The α-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase family (GH115).'' Appl Microbiol Biotechnol. 2011 May;90(4):1323-1332. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1007/s00253-011-3157-y DOI:10.1007/s00253-011-3157-y] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21442271 PMID: 21442271]
 </biblio>

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 #Tenkanen2000 pmid=10725538
 #Ryabova2009 pmid=19344716
-#Kolenova2010 Kolenová K, Ryabova O, Vrsanská M, Biely P. ''Inverting character of family GH115 α-glucuronidases.'' FEBS Lett. 2010 Sep 24;584(18):4063-4068. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1016/j.febslet.2010.08.031 DOI:10.1016/j.febslet.2010.08.031] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20804758 PMID: 20804758]
+#Kolenova2010 pmid=20804758
 #Fujimoto2011 Fujimoto Z, Ichinose H, Biely P, Kaneko S. ''Crystallization and preliminary crystallographic analysis of the glycoside hydrolase family 115 α-glucuronidase from Streptomyces pristinaespiralis.'' Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jan 1;67(Pt 1):68-71. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1107/S1744309110043721 DOI:10.1107/S1744309110043721] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21206027 PMID: 21206027]
 #Chong2011 Chong SL, Battaglia E, Coutinho PM, Henrissat B, Tenkanen M, de Vries RP. ''The α-glucuronidase Agu1 from Schizophyllum commune is a member of a novel glycoside hydrolase family (GH115).'' Appl Microbiol Biotechnol. 2011 May;90(4):1323-1332. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1007/s00253-011-3157-y DOI:10.1007/s00253-011-3157-y] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21442271 PMID: 21442271]

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 == Substrate specificities ==
-[[Glycoside hydrolases]] of GH115 display alpha-glucuronidase activity. In particular, members of this family catalyze the cleavage of 4-''O''-methyl D-glucuronic acid sidechains from native xylan polysaccharides (EC [{{EClink}}3.2.1.131 3.2.1.131)]. In contrast to [[GH67]] enzymes, which only cleave glucuronosyl linkages at the non-reducing ends of xylooligosaccharides, GH115 enzymes remove glucuronic acid from the both terminal and internal regions of xylooligosaccharides and xylans <cite>Ryabova2009</cite>. This substrate specificity was first demonstrated by an alpha-glucuronidase purified from ''Thermoascus aurantiacus'' <cite>Khandke1989</cite>, and later for a ''Schizophyllum commune'' alpha-glucuronidase <cite>Tenkanen2000</cite>. Although GH115 was established on the basis of biochemical and sequence analysis of ''Pichia stipitis'' (4-''O''-methyl)-alpha-glucuronidase <cite>Ryabova2009</cite>, available N-terminal protein sequence of the ''S. commune'' enzyme  <cite>Tenkanen2000</cite> allowed the tentative assignment of this enzyme to GH115 <cite>Ryabova2009</cite>, which was later confirmed by the full protein sequence <cite>Chong2011</cite>.  A GH115 member from ''Streptomyces pristinaespiralis'' produces both 4-''O''-methyl-D-glucuronic acid and non-methylated D-glucuronic acid from xylan and xylo-oligosaccharides <cite>Fujimoto2011</cite>.
+[[Glycoside hydrolases]] of GH115 display α-glucuronidase activity. In particular, members of this family catalyze the cleavage of 4-''O''-methyl D-glucuronic acid sidechains from native xylan polysaccharides (EC [{{EClink}}3.2.1.131 3.2.1.131)]. In contrast to [[GH67]] enzymes, which only cleave glucuronosyl linkages at the non-reducing ends of xylooligosaccharides, GH115 enzymes remove glucuronic acid from the both terminal and internal regions of xylooligosaccharides and xylans <cite>Ryabova2009</cite>. This substrate specificity was first demonstrated by an α-glucuronidase purified from ''Thermoascus aurantiacus'' <cite>Khandke1989</cite>, and later for a ''Schizophyllum commune'' α-glucuronidase <cite>Tenkanen2000</cite>. Although GH115 was established on the basis of biochemical and sequence analysis of ''Pichia stipitis'' (4-''O''-methyl)-α-glucuronidase <cite>Ryabova2009</cite>, available N-terminal protein sequence of the ''S. commune'' enzyme  <cite>Tenkanen2000</cite> allowed the tentative assignment of this enzyme to GH115 <cite>Ryabova2009</cite>, which was later confirmed by the full protein sequence <cite>Chong2011</cite>.  A GH115 member from ''Streptomyces pristinaespiralis'' produces both 4-''O''-methyl-D-glucuronic acid and non-methylated D-glucuronic acid from xylan and xylo-oligosaccharides <cite>Fujimoto2011</cite>.
 == Kinetics and Mechanism ==
-Using reduced aldopentauronic acid (MeGlcA3Xyl4-ol) as a substrate, analysis by <sup>1</sup>H-NMR spectroscopy revealed that the enzymes from both ''S. commune'' and ''P. stipitis'' release the beta-anomer of 4-O-methyl-D-glucuronic acid (MeGlcA) as the first-formed product, thus suggesting a one step, [[inverting]] mechanism <cite>Kolenova2010</cite>.
+Using reduced aldopentauronic acid (MeGlcA3Xyl4-ol) as a substrate, analysis by <sup>1</sup>H-NMR spectroscopy revealed that the enzymes from both ''S. commune'' and ''P. stipitis'' release the β-anomer of 4-O-methyl-D-glucuronic acid (MeGlcA) as the first-formed product, thus suggesting a one step, [[inverting]] mechanism <cite>Kolenova2010</cite>.
 == Catalytic Residues ==
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 == Family Firsts ==
-;First stereochemistry determination: Release of the beta-anomer of 4-methyl-D-glucuronic acid by both the ''Schizophyllum commune'' and ''Pichia stipitis'' enzymes using <sup>1</sup>H NMR <cite>Kolenova2010</cite>.
+;First stereochemistry determination: Release of the β-anomer of 4-methyl-D-glucuronic acid by both the ''Schizophyllum commune'' and ''Pichia stipitis'' enzymes using <sup>1</sup>H NMR <cite>Kolenova2010</cite>.
 ;First [[general acid]] residue identification: Not yet identified.
 ;First [[general base]] residue identification: Not yet identified.

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 == Family Firsts ==
-;First stereochemistry determination: 1H NMR demonstrated that the released 4-methyl-D-glucuronic acid was a beta anomer and thus that the enzyme is an inverter <cite>Kolenova2010</cite>.
+;First stereochemistry determination: Release of the beta-anomer of 4-methyl-D-glucuronic acid by both the ''Schizophyllum commune'' and ''Pichia stipitis'' enzymes using <sup>1</sup>H NMR <cite>Kolenova2010</cite>.
 ;First catalytic nucleophile identification: Not yet identified.
 ;First general acid/base residue identification: Not yet identified.
-;First 3-D structure: Just crystallization of S. pristinaespiralis enzyme is reported <cite>Fujimoto2011</cite>.
+;First 3-D structure: Only the crystallization of the ''Streptomyces pristinaespiralis'' family member has been reported <cite>Fujimoto2011</cite>.
 == References ==

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 == Kinetics and Mechanism ==
-Using 1H NMR spectroscopy and reduced aldopentaouronic acid(MeGlcA3Xyl4-ol) as a substrate, it was demonstrated that both the enzymes from S. commune and P. stipitis releasing 4-O-methyl-D-glucuronic acid (MeGlcA) as its beta-anomer, suggesting a single displacement mechanism <cite>Kolenova2010</cite>.
+Using reduced aldopentaouronic acid(MeGlcA3Xyl4-ol) as a substrate, <sup>1</sup>H-NMR spectroscopy demonstrated that both the enzymes from ''S. commune'' and ''P. stipitis'' released the beta-anomer of 4-O-methyl-D-glucuronic acid (MeGlcA) as the first-formed product, thus suggesting a single displacement, [[inverting]] mechanism <cite>Kolenova2010</cite>.
 == Catalytic Residues ==