Glycoside Hydrolase Family 121 - Revision history

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

2021-12-18T21:18:46Z

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

Harry Brumer: /* Family Firsts */

2020-08-06T19:36:24Z

Family Firsts

Harry Brumer at 19:36, 6 August 2020

2020-08-06T19:36:01Z

Harry Brumer at 18:18, 6 August 2020

2020-08-06T18:18:34Z

Harry Brumer: /* Three-dimensional structures */

2020-08-06T18:15:57Z

Three-dimensional structures

Shinya Fushinobu: Crystal structure paper updated.

2020-08-06T08:55:19Z

Crystal structure paper updated.

Spencer Williams at 01:41, 26 November 2012

2012-11-26T01:41:43Z

Harry Brumer: /* Substrate specificities */

2012-11-12T20:44:50Z

Substrate specificities

Harry Brumer: added GH127 cross reference

2012-11-12T20:42:33Z

added GH127 cross reference

Harry Brumer: /* Substrate specificities */

2012-11-12T20:39:49Z

Substrate specificities

@@ 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]]
 ----

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 == Family Firsts ==
-;First stereochemistry determination:  Shown to be [[retaining]] for HypBA2 enzyme by product analysis of glycosyl transfer reactions to methanol <cite>Fujita2011A</cite>.
+;First stereochemistry determination:  Shown to be [[retaining]] for HypBA2 by product analysis of glycosyl transfer reactions to methanol <cite>Fujita2011A</cite>.
 ;First catalytic nucleophile identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof.
 ;First general acid/base residue identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof.

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 == Kinetics and Mechanism ==
-HypBA2 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol; the resulting Ara''f''&beta;1-2Ara''f''&beta;-Me was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis.
+HypBA2 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol; the resulting Ara''f''&beta;1-2Ara''f''&beta;-Me was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2011A</cite>.
 == Catalytic Residues ==
@@ Line 40: / Line 40: @@
 == Family Firsts ==
-;First stereochemistry determination:  Shown to be [[retaining]] for HypBA2 enzyme by measurement of glycosyl transfer reactions to methanol and the <sup>1</sup>H-NMR and <sup>13</sup>C-NMR spectra <cite>Fujita2011A</cite>.
+;First stereochemistry determination:  Shown to be [[retaining]] for HypBA2 enzyme by product analysis of glycosyl transfer reactions to methanol <cite>Fujita2011A</cite>.
 ;First catalytic nucleophile identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof.
 ;First general acid/base residue identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof.

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 </div>
 <!-- This is the end of the table -->
 == Substrate specificities ==
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 == Family Firsts ==
 ;First stereochemistry determination:  Shown to be [[retaining]] for HypBA2 enzyme by measurement of glycosyl transfer reactions to methanol and the <sup>1</sup>H-NMR and <sup>13</sup>C-NMR spectra <cite>Fujita2011A</cite>.
-;First catalytic nucleophile identification: No experimental proof.
+;First catalytic nucleophile identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof.
-;First general acid/base residue identification: No experimental proof.
+;First general acid/base residue identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof.
 ;First 3-D structure: &beta;-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' <cite>Saito2020</cite>.

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 == Three-dimensional structures ==
-[[Image:GH121-HypBA2.png|'''Figure 1:''' &beta;-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum''. The catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain is in green.|frame|right]]
+[[File:GH121-HypBA2.png|thumb|300px|right|'''Figure 1:''' &beta;-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum''. The catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain is in green.]]
 The first solved 3-D structure was &beta;-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' (PDB [{{PDBlink}}6m5a 6M5A]) <cite>Saito2020</cite>. The catalytic domain adops an (&alpha;/&alpha;)<sub>6</sub> barrel fold similar to [[GH142]], [[GH63]], [[GH78]], [[GH94]], and [[GH37]] ('''Figure 1''').
 == Family Firsts ==

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 == Catalytic Residues ==
-Not known.
+The catalytic residues are not known but three conserved residues (Glu373, Asp515, and Glu713 in ''B. longum'' HypBA2) are the candidates based on mutagenesis and structural comparison <cite>Saito2020</cite>.
 == Three-dimensional structures ==
-Not known.
+[[Image:GH121-HypBA2.png|'''Figure 1:''' &beta;-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum''. The catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain is in green.|frame|right]]
 == Family Firsts ==
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 ;First catalytic nucleophile identification: No experimental proof.
 ;First general acid/base residue identification: No experimental proof.
-;First 3-D structure: Not known.
+;First 3-D structure: &beta;-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' <cite>Saito2020</cite>.
 == References ==
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 #Fujita2011A pmid=21149454
 #Fujita2011B pmid=21914802
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH121]]

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 == Substrate specificities ==
-This family of [[glycoside hydrolases]] contains &beta;-L-arabinobiosidases, as demonstrated for HypBA2 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011A</cite>. HypBA2 liberates the disaccharide Ara''f''&beta;1-2Ara''f'' (&beta;-Ara<sub>2</sub>, a substrate of the [[GH127]] &beta;-L-arabinofuranosidase from ''B. longum'' JCM 1217 <cite>Fujita2011B</cite>) from unmodified Ara''f''&beta;1-2Ara''f''&beta;1-2Ara''f''&beta;-hydroxyproline (Ara<sub>3</sub>-Hyp) but not Ara''f''&alpha;1-3Ara''f''&beta;1-2Ara''f''&beta;1-2Ara''f''&beta;-Hyp (Ara<sub>4</sub>-Hyp) or Ara''f''&beta;1-2Ara''f''&beta;-Hyp (Ara<sub>2</sub>-Hyp). HypBA2 directly liberates &beta;-Ara<sub>2</sub> from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin. The family members are only found from prokaryote genomes, such as bacteria and actinomycetes.
+This family of [[glycoside hydrolases]] contains &beta;-L-arabinobiosidases, as demonstrated for HypBA2 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011A</cite>. HypBA2 liberates the disaccharide Ara''f''&beta;1-2Ara''f'' (&beta;-Ara<sub>2</sub>, a substrate of the [[GH127]] &beta;-L-arabinofuranosidase from ''B. longum'' JCM 1217 <cite>Fujita2011B</cite>) from unmodified Ara''f''&beta;1-2Ara''f''&beta;1-2Ara''f''&beta;-hydroxyproline (Ara<sub>3</sub>-Hyp), but not Ara''f''&alpha;1-3Ara''f''&beta;1-2Ara''f''&beta;1-2Ara''f''&beta;-Hyp (Ara<sub>4</sub>-Hyp) or Ara''f''&beta;1-2Ara''f''&beta;-Hyp (Ara<sub>2</sub>-Hyp). HypBA2 directly liberates &beta;-Ara<sub>2</sub> from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin. The family members are only found from prokaryote genomes, such as bacteria and actinomycetes.
 == Kinetics and Mechanism ==