Glycoside Hydrolase Family 63 - Revision history

Takatsugu Miyazaki at 06:00, 12 July 2023

2023-07-12T06:00:45Z

Takatsugu Miyazaki at 05:59, 12 July 2023

2023-07-12T05:59:50Z

Takatsugu Miyazaki at 05:57, 12 July 2023

2023-07-12T05:57:40Z

Harry Brumer: added User:Takatsugu Miyazaki as co-author, according to email request from User:Takashi Tonozuka

2023-01-10T15:50:47Z

added User:Takatsugu Miyazaki as co-author, according to email request from User:Takashi Tonozuka

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

2021-12-18T21:19:42Z

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

Takashi Tonozuka at 11:18, 8 April 2013

2013-04-08T11:18:34Z

Takashi Tonozuka at 11:04, 8 April 2013

2013-04-08T11:04:38Z

Takashi Tonozuka at 10:33, 8 April 2013

2013-04-08T10:33:57Z

Takashi Tonozuka at 10:31, 8 April 2013

2013-04-08T10:31:16Z

Takashi Tonozuka at 10:26, 8 April 2013

2013-04-08T10:26:29Z

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 #Nobre2013 pmid=23179444
-#Alarico2014 pmid=
+#Alarico2014 pmid=25341489
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH063]]

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 In 2013, the substrates of GH63 enzymes from ''Thermus thermophilus'' HB27 and ''Rubrobacter radiotolerans'' RSPS-4 were identified as compatible solutes, &alpha;-D-mannopyranosyl-1,2-D-glycerate (mannosylglycerate) and &alpha;-D-glucopyranosyl-1,2-D-glycerate (glucosylglycerate) <cite>Alarico2013</cite>. Subsequently, glucosylglycerate hydrolase was identified in ''Mycobacterium hassiacum'' and was found to be involved in the recovery process from nitrogen starvation by hydrolyzing glucosylglycerate <cite>Alarico2014</cite>.
-An orthologous gene for mannosyl/glucosylglycerate hydrolase was found in the genome of plant ''Selaginella moellendorffii'', and the gene product hydrolyzed these compatible solutes <cite>Nobre2013</cite>.
+An orthologous gene for mannosyl/glucosylglycerate hydrolase was also found in the genome of plant ''Selaginella moellendorffii'', and the gene product hydrolyzed these compatible solutes <cite>Nobre2013</cite>.
 == Kinetics and Mechanism ==
 Family GH63 enzymes are [[inverting]] enzymes, as first shown by NMR on a processing &alpha;-glucosidase I from ''S. cerevisiae'' <cite>Palcic1999</cite>.

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 [[Glycoside hydrolases]] of GH63 are exo-acting &alpha;-glucosidases. Eukaryotic members of this family are processing &alpha;-glucosidase I enzymes (mannosyl-oligosaccharide glucosidase, EC [{{EClink}}3.2.1.106 3.2.1.106]), which specifically hydrolyze the terminal &alpha;-1,2-glucosidic linkage in the ''N''-linked oligosaccharide precursor, Glc<sub>3</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>, to produce &beta;-glucose and Glc<sub>2</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>. Processing &alpha;-glucosidase I thus plays a critical role in the maturation of eukaryotic ''N''-glycans. The enzymatic properties of Cwh41p, a processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'', have been intensively studied <cite>Dhanawansa2002</cite> (also reviewed in <cite>Herscovics1999</cite>).
-Genes encoding GH63 enzymes have also been found in archaea and bacteria, but their natural substrates are still unclear, as these organisms are not known to produce eukaryotic ''N''-linked oligosacharides. A bacterial GH63 enzyme, ''Escherichia coli'' YgjK, demonstrated the highest activity toward the &alpha;-1,3-glucosidic linkage of nigerose (Glc-&alpha;-1,3-Glc) among the commercially available sugars tested, but the Km value for nigerose was substantially higher than that for other typical &alpha;-glucosidases  <cite>Kurakata2008</cite>. In 2013, the substrates of GH63 enzymes from ''Thermus thermophilus'' HB27 and ''Rubrobacter radiotolerans'' RSPS-4 have been identified as &alpha;-D-mannopyranosyl-1,2-D-glycerate (mannosylglycerate) and &alpha;-D-glucopyranosyl-1,2-D-glycerate (glucosylglycerate) <cite>Alarico2013</cite>.
+Genes encoding GH63 enzymes have also been found in archaea and bacteria, but their natural substrates are still unclear, as these organisms are not known to produce eukaryotic ''N''-linked oligosacharides. A bacterial GH63 enzyme, ''Escherichia coli'' YgjK, demonstrated the highest activity toward the &alpha;-1,3-glucosidic linkage of nigerose (Glc-&alpha;-1,3-Glc) among the commercially available sugars tested, but the ''K''<sub>m</sub> value for nigerose was substantially higher than that for other typical &alpha;-glucosidases  <cite>Kurakata2008</cite>. The aglycon specificity of YgjK was screened using its glycosynthase mutants (D324N and E727A), which synthesized 2-''O''-α-glucopyranosylgalactose from β-glucopyranosyl fluoride donor and galactose acceptor <cite>Miyazaki2013</cite>.
 == Kinetics and Mechanism ==
 Family GH63 enzymes are [[inverting]] enzymes, as first shown by NMR on a processing &alpha;-glucosidase I from ''S. cerevisiae'' <cite>Palcic1999</cite>.
@@ Line 60: / Line 63: @@
 #Stam2005 pmid=16226731
 #Kalz-Fuller1995 pmid=7635146
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH063]]

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 {{CuratorApproved}}
-* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]
+* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]
 * [[Responsible Curator]]:  [[User:Takashi Tonozuka|Takashi Tonozuka]]
 ----

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Takashi Tonozuka^^^
+* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]
-* [[Responsible Curator]]:  ^^^Takashi Tonozuka^^^
+* [[Responsible Curator]]:  [[User:Takashi Tonozuka|Takashi Tonozuka]]
 ----

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 == Three-dimensional structures ==
-The crystal structures of the bacterial GH63 proteins, ''E. coli'' YgjK <cite>Kurakata2008</cite> ([http://www.cazy.org/GH63_structure.html multiple PDB entries]) and ''Thermus thermophilus'' uncharacterised protein TTHA0978 ([{{PDBlink}}2z07 PDB 2z07]), have been reported. The catalytic domain consists of an (&alpha;/&alpha;)<sub>6</sub> barrel fold. The main chain of the (&alpha;/&alpha;)<sub>6</sub> barrel domain shares high structural similarity with those of [[GH15]], [[GH37]], [[GH65]], and [[GH94]] <cite>Kurakata2008 Gibson2007</cite>. This similarity had been predicted on the basis of sequence comparison, before their crystal structures were available <cite>Stam2005</cite>.
+The crystal structures of the bacterial GH63 proteins, ''E. coli'' YgjK <cite>Kurakata2008</cite> ([http://www.cazy.org/GH63_structure.html multiple PDB entries]) and ''Thermus thermophilus'' uncharacterised protein TTHA0978 ([{{PDBlink}}2z07 PDB 2z07]), have been reported. The catalytic domain consists of an (&alpha;/&alpha;)<sub>6</sub> barrel fold. The main chain of the (&alpha;/&alpha;)<sub>6</sub> barrel domain shares high structural similarity with those of [[GH15]], [[GH37]], [[GH65]], and [[GH94]] <cite>Kurakata2008 Gibson2007</cite>. This similarity had been predicted on the basis of sequence comparison, before their crystal structures were available <cite>Stam2005</cite>. The first crystal structure of the eukaryotic processing &alpha;-glucosidase I ([{{PDBlink}}4j5t PDB 4j5t]) has been reported in 2013 <cite>Barker2013</cite>.
 == Family Firsts ==

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 ;First general base residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.
 ;First 3-D structure: ''Escherichia coli'' YgjK, an enzyme showing the highest activity for the &alpha;-1,3-glucosidic linkage of nigerose <cite>Kurakata2008</cite>.
 == References ==

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 <biblio>
 #Alarico2013 pmid=23273275
 #Dhanawansa2002 pmid=11971867
 #Herscovics1999 pmid=9878780