Glycoside Hydrolase Family 130 - Revision history

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

2021-12-18T21:15:45Z

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

Spencer Williams at 10:36, 19 September 2019

2019-09-19T10:36:55Z

Spencer Williams at 12:47, 18 September 2019

2019-09-18T12:47:30Z

Harry Brumer: /* Kinetics and Mechanism */

2018-02-16T09:41:15Z

Kinetics and Mechanism

Harry Brumer: /* Substrate specificities */

2018-02-16T09:40:56Z

Substrate specificities

Harry Brumer at 09:40, 16 February 2018

2018-02-16T09:40:17Z

Wataru Saburi: /* References */

2018-02-16T02:40:16Z

References

Wataru Saburi: /* Catalytic Residues */

2018-02-16T02:35:51Z

Catalytic Residues

Wataru Saburi: /* Catalytic Residues */

2018-02-16T02:34:40Z

Catalytic Residues

Wataru Saburi: /* Kinetics and Mechanism */

2018-02-16T02:29:39Z

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]]: ^^^Wataru Saburi^^^
+* [[Author]]: [[User:Wataru Saburi|Wataru Saburi]]
-* [[Responsible Curator]]:  ^^^Haruhide Mori^^^
+* [[Responsible Curator]]:  [[User:Haruhide Mori|Haruhide Mori]]
 ----

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 |-
 |'''Clan'''
-|with GT108, the first GH/GT clan
+|GH-S
 |-
 |'''Mechanism'''

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 |-
 |'''Clan'''
-|none
+|with GT108, the first GH/GT clan
 |-
 |'''Mechanism'''

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 == Kinetics and Mechanism ==
-GH130 phosphorylases phosphorolyze &beta;-mannosidic linkages at the non-reducing end of substrates with net [[inverting|inversion]] of anomeric configuration affording &alpha;-mannose-1-phosphate. Senoura et al. <cite>Senoura2011</cite> demonstrated that 4-''O''-&beta;-D-mannosyl-D-glucose phosphorylase from ''Bacteroides fragilis'' (BfMGP) produces &alpha;-mannose 1-phosphate and glucose from 4-''O''-&beta;-D-mannosyl-D-glucose and inorganic phosphate. A unique proton relay mechanism for GH130 enzymes was proposed on the basis of the three-dimensional strucuture of BfMGP <cite>Nakae2013</cite>. In contrast to other inverting glycoside phosphorylases, where a general acid catalyst is proposed to directly protonate the glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is transferred intramolecularly to the glycosidic oxygen from 3OH group. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and &alpha;-mannose 1-phosphate is generated. &beta;-1,2-Mannosidase lacks some basic amino acid residues responsible for binding to inorganic phosphate in phosphorylases, but has two Glu residues acting as general base catalyst <cite>Cuskin2015</cite> <cite>Nihira2015</cite>. These residues could activate catalytic water to facilitate nucleophilic attack to the anomeric carbon of the mannosyl residue.
+GH130 phosphorylases phosphorolyze &beta;-mannosidic linkages at the non-reducing end of substrates with net [[inverting|inversion]] of anomeric configuration affording &alpha;-mannose-1-phosphate. Senoura et al. <cite>Senoura2011</cite> demonstrated that 4-''O''-&beta;-D-mannosyl-D-glucose phosphorylase from ''Bacteroides fragilis'' (BfMGP) produces &alpha;-mannose 1-phosphate and glucose from 4-''O''-&beta;-D-mannosyl-D-glucose and inorganic phosphate. A unique proton relay mechanism for GH130 enzymes was proposed on the basis of the three-dimensional strucuture of BfMGP <cite>Nakae2013</cite>. In contrast to other inverting glycoside phosphorylases, where a general acid catalyst is proposed to directly protonate the glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is transferred intramolecularly to the glycosidic oxygen from 3OH group. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and &alpha;-mannose 1-phosphate is generated. &beta;-1,2-Mannosidase lacks some basic amino acid residues responsible for binding to inorganic phosphate in phosphorylases, but has two Glu residues acting as general base catalyst <cite>Cuskin2015 Nihira2015</cite>. These residues could activate catalytic water to facilitate nucleophilic attack to the anomeric carbon of the mannosyl residue.
 == Catalytic Residues ==

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 == Substrate specificities ==
-Family [[GH130]]  contains [[phosphorylases]] and a [[glycoside hydrolase]] acting on &beta;-mannosides. This family was created based on the identification of 4-''O''-&beta;-D-mannosyl-D-glucose phosphorylase activity (EC [{{EClink}}2.4.1.281 2.4.1.281]) for the protein (BfMGP) derived from the gene BF0772 of ''Bacteroides fragilis'' <cite>Senoura2011</cite>. This enzyme is likely involved in the degradation of &beta;-1,4-mannobiose together with cellobiose 2-epimerase, which converts &beta;-1,4-mannobiose to 4-''O''-&beta;-D-mannosyl-D-glucose. Other activities within the family include: &beta;-1,4-mannooligosaccharide phosphorylase (EC [{{EClink}}2.4.1.319 2.4.1.319]) <cite>Kawahara2012</cite>, 1,4-&beta;-mannosyl-''N''-acetylglucosamine phosphorylase (EC [{{EClink}}2.4.1.320 2.4.1.320]) <cite>Nihira2013</cite>  <cite>Ladeveze2013</cite>, 1,2-&beta;-oligomannan phosphorylase <cite>Chiku2014</cite>, &beta;-1,2-mannnobiose phosphorylase <cite>Chiku2014</cite>, and &beta;-1,2-mannosidase <cite>Cuskin2015</cite> <cite>Nihira2015</cite>
+Family [[GH130]]  contains [[phosphorylases]] and a [[glycoside hydrolase]] acting on &beta;-mannosides. This family was created based on the identification of 4-''O''-&beta;-D-mannosyl-D-glucose phosphorylase activity (EC [{{EClink}}2.4.1.281 2.4.1.281]) for the protein (BfMGP) derived from the gene BF0772 of ''Bacteroides fragilis'' <cite>Senoura2011</cite>. This enzyme is likely involved in the degradation of &beta;-1,4-mannobiose together with cellobiose 2-epimerase, which converts &beta;-1,4-mannobiose to 4-''O''-&beta;-D-mannosyl-D-glucose. Other activities within the family include: &beta;-1,4-mannooligosaccharide phosphorylase (EC [{{EClink}}2.4.1.319 2.4.1.319]) <cite>Kawahara2012</cite>, 1,4-&beta;-mannosyl-''N''-acetylglucosamine phosphorylase (EC [{{EClink}}2.4.1.320 2.4.1.320]) <cite>Nihira2013 Ladeveze2013</cite>, 1,2-&beta;-oligomannan phosphorylase <cite>Chiku2014</cite>, &beta;-1,2-mannnobiose phosphorylase <cite>Chiku2014</cite>, and &beta;-1,2-mannosidase <cite>Cuskin2015 Nihira2015</cite>
 == Kinetics and Mechanism ==

← Older revision		Revision as of 02:40, 16 February 2018
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	#Nihira2013 pmid=23943617		#Nihira2013 pmid=23943617
		+
		+	#Cuskin2015 pmid=26286752
		+
		+	#Nihira2015 pmid=26476324
		+
		+
	#Chiku2014 pmid=25500577		#Chiku2014 pmid=25500577

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 == Catalytic Residues ==
-Ladevèze et al. <cite>Ladeveze2013</cite> compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Mutation of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation completely abolished the catalytic activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the glycosidic oxygen <cite>Nakae2013</cite>. However, this Asp appeared to be too distant from the the glycosidic oxygen for direct protonation, and the proton relay mechanism described above was therefore proposed. In &beta;-1,2-Mannosidase from Dyadobacter fermentans, Glu224 and Glu265 act as general base catalyst <cite>Nihira2015</cite> to activate catalytic water.
+Ladevèze et al. <cite>Ladeveze2013</cite> compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Mutation of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation completely abolished the catalytic activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the glycosidic oxygen <cite>Nakae2013</cite>. However, this Asp appeared to be too distant from the the glycosidic oxygen for direct protonation, and the proton relay mechanism described above was therefore proposed. In &beta;-1,2-mannosidase from ''Dyadobacter fermentans'', Glu224 and Glu265 act as general base catalyst <cite>Nihira2015</cite> to activate catalytic water.
 == Three-dimensional structures ==