Glycoside Hydrolase Family 127 - Revision history

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

2021-12-18T21:18:46Z

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

Harry Brumer at 15:51, 27 July 2015

2015-07-27T15:51:26Z

Harry Brumer at 15:48, 27 July 2015

2015-07-27T15:48:45Z

Harry Brumer at 15:44, 27 July 2015

2015-07-27T15:44:39Z

Kiyotaka Fujita at 05:52, 27 July 2015

2015-07-27T05:52:06Z

Kiyotaka Fujita: Undo revision 10685 by Kiyotaka Fujita (talk)

2015-07-27T05:36:13Z

Undo revision 10685 by Kiyotaka Fujita (talk)

Kiyotaka Fujita: Undo revision 10686 by Kiyotaka Fujita (talk)

2015-07-27T04:43:30Z

Undo revision 10686 by Kiyotaka Fujita (talk)

Kiyotaka Fujita at 23:42, 19 July 2015

2015-07-19T23:42:17Z

Kiyotaka Fujita at 23:39, 19 July 2015

2015-07-19T23:39:49Z

Shinya Fushinobu at 05:15, 11 September 2014

2014-09-11T05:15:42Z

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

@@ Line 36: / Line 36: @@
 * Ara''f''&beta;1-2Ara''f''&beta;-Me
-The members of GH127 are also members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants.  Establishment of GH127 by biochemical analysis thus resolved the "domain of unknown function" status of this PFAM family.
+The members of GH127 were previosuly known as members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants.  Establishment of GH127 by biochemical analysis thus resolved the "domain of unknown function" status of this PFAM family.
 ''Note: The original paper describing ''B. longum'' HypBA1 as the founding member of GH127 <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and a revised version was published in 2014 <cite>Fujita2014</cite>, to correct errors due to an inadvertent mix-up of sample tubes and data for the E338A and E366A mutants.''

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-This family of [[glycoside hydrolases]] contains &beta;-L-arabinofuranosidase activity, which was established for HypBA1 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011B Fujita2013 Fujita2014</cite>. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin:
+This family of [[glycoside hydrolases]] contains &beta;-L-arabinofuranosidase activity, which was established for HypBA1 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2014</cite>. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin:
 * Ara''f''&beta;1-2Ara''f'' (&beta;-Ara<sub>2</sub>, a product of the [[GH121]] &beta;-L-arabinobiosidase from ''B. longum'' JCM 1217 <cite>Fujita2011A</cite>)
 * Ara''f''&beta;-hydroxyproline (Ara-Hyp)
@@ Line 36: / Line 36: @@
 * Ara''f''&beta;1-2Ara''f''&beta;-Me
-The members of GH127 are also members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants.  Establishment of GH127 by biochemical analysis thus resolves the "domain of unknown function" status of this PFAM family.
+The members of GH127 are also members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants.  Establishment of GH127 by biochemical analysis thus resolved the "domain of unknown function" status of this PFAM family.
-''Note: The original paper describing 'B. longum'' HypBA1 as the founding member of GH127 <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and a revised version was published <cite>Fujita2014</cite>, to correct errors due to an inadvertent mix-up of sample tubes and data for the E338A and E366A mutants.''
+''Note: The original paper describing ''B. longum'' HypBA1 as the founding member of GH127 <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and a revised version was published in 2014 <cite>Fujita2014</cite>, to correct errors due to an inadvertent mix-up of sample tubes and data for the E338A and E366A mutants.''
 == Kinetics and Mechanism ==
-HypBA1 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl &beta;-L-arabinofuranoside was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2011B Fujita2013 Fujita2014</cite>
+HypBA1 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl &beta;-L-arabinofuranoside was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2014</cite>
 == Catalytic Residues ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-This family of [[glycoside hydrolases]] contains &beta;-L-arabinofuranosidase activity, which was established for HypBA1 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011B</cite><cite>Fujita2013</cite><cite>Fujita2014</cite>. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin:
+This family of [[glycoside hydrolases]] contains &beta;-L-arabinofuranosidase activity, which was established for HypBA1 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011B Fujita2013 Fujita2014</cite>. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin:
 * Ara''f''&beta;1-2Ara''f'' (&beta;-Ara<sub>2</sub>, a product of the [[GH121]] &beta;-L-arabinobiosidase from ''B. longum'' JCM 1217 <cite>Fujita2011A</cite>)
 * Ara''f''&beta;-hydroxyproline (Ara-Hyp)
@@ Line 37: / Line 37: @@
 The members of GH127 are also members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants.  Establishment of GH127 by biochemical analysis thus resolves the "domain of unknown function" status of this PFAM family.
 == Kinetics and Mechanism ==
-HypBA1 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl &beta;-L-arabinofuranoside was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2011B</cite><cite>Fujita2013</cite><cite>Fujita2014</cite>.
+HypBA1 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl &beta;-L-arabinofuranoside was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2011B Fujita2013 Fujita2014</cite>
 == Catalytic Residues ==
@@ Line 61: / Line 63: @@
 #Ito2014 pmid=24680821
 </biblio>
-Because the results of E338A and E366A mutants of HypBA1 were reversely reported by mixing up the sample tubes inadvertently, the paper <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and resubmited in 2014 <cite>Fujita2014</cite>.
 [[Category:Glycoside Hydrolase Families|GH127]]

@@ Line 61: / Line 61: @@
 #Ito2014 pmid=24680821
 </biblio>
-Because the results of E338A and E366A mutants of HypBA1 were reversely reported by mixing up the sample tubes inadvertently, the paper <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and resubmited a corrected manuscript in 2014 <cite>Fujita2014</cite>.
+Because the results of E338A and E366A mutants of HypBA1 were reversely reported by mixing up the sample tubes inadvertently, the paper <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and resubmited in 2014 <cite>Fujita2014</cite>.
 [[Category:Glycoside Hydrolase Families|GH127]]

@@ Line 55: / Line 55: @@
 == References ==
 <biblio>
 #Fujita2014 pmid=24385433
 #Ito2014 pmid=24680821
 </biblio>

@@ Line 17: / Line 17: @@
 |-
 |'''Active site residues'''
-|not known
+|known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 42: / Line 42: @@
 == Catalytic Residues ==
-Not known.
+In the crystal structure of HypBA1, a Zn<sup>2+</sup> ion was bound to the active site <cite>Ito2014</cite>. A cysteine residue (Cys417), which is involved in the coordination of the Zn<sup>2+</sup>, was suggested to act as the nucleophile. Glu322 is possibly the acid/base catalyst. A possible reaction mechanism involving the cysteine residue as the nucleophile was suggested based on crystal structures, site-directed mutagenesis, some biochemical analysis, and quantum mechanical calculations <cite>Ito2014</cite>.
 == Three-dimensional structures ==
-Not known.
+HypBA1 from ''B. longum'' JCM 1217 <cite>Ito2014</cite>. It consists of a catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain and two additional &beta;-sandwich domains.
 == Family Firsts ==
 ;First stereochemistry determination: This was determined with HypBA1 enzyme by measurement of glycosyl transfer reactions to methanol and the <sup>1</sup>H-NMR and<sup>13</sup>C-NMR spectra  <cite>Fujita2011B</cite>.
-;First catalytic nucleophile identification: No experimental proof.
+;First [[catalytic nucleophile]] identification:
-;First general acid/base residue identification: No experimental proof.
+;First [[general acid/base]] residue identification:
-;First 3-D structure: Not known.
+;First 3-D structure: HypBA1 from ''B. longum'' JCM 1217 by X-ray crystallography <cite>Ito2014</cite>.
 == References ==
@@ Line 57: / Line 57: @@
 #Fujita2011A pmid=21149454
 #Fujita2011B pmid=21914802
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH127]]