Glycoside Hydrolase Family 113 - Revision history

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

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Spencer Williams at 22:54, 2 January 2014

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Spencer Williams at 19:09, 18 December 2013

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Spencer Williams at 19:08, 18 December 2013

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Spencer Williams at 19:07, 18 December 2013

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Spencer Williams at 19:06, 18 December 2013

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Spencer Williams at 03:00, 15 December 2013

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Spencer Williams at 20:29, 14 December 2013

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Spencer Williams at 20:27, 14 December 2013

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 {{CuratorApproved}}
-* [[Author]]s: ^^^Rohan Williams^^^ and ^^^Spencer Williams^^^
+* [[Author]]s: [[User:Rohan Williams|Rohan Williams]] and [[User:Spencer Williams|Spencer Williams]]
-* [[Responsible Curator]]: ^^^Spencer Williams^^^
+* [[Responsible Curator]]: [[User:Spencer Williams|Spencer Williams]]
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 == Substrate specificities ==
-Only a single [[glycoside hydrolase]] of family [[GH113]] has been characterized, intracellular ''Aa''ManA from ''Alicyclobacillus acidocaldarius'' Tc-12-31 <cite>Zhang2008</cite>. This thermoacidophilic organism was originally selected for its ability to hydrolyse konjac glucomannan <cite>Zhang2008</cite>. The recombinantly-expressed enzyme possessed activity against polysaccharides containing &beta;-1,4-mannosidic linkages, including significant activity against konjac glucomannan, and galactomannan from locust bean gum. Some activity was also observed against crystalline ivory nut mannan (an unsubstituted &beta;-1,4-mannan) and guar gum (a more highly-substituted galactomannan) <cite>Zhang2008</cite>. No activity was observed against the other polysaccharides and ''p''-nitrophenyl glycosides tested, including ''p''-nitrophenyl &beta;- and &alpha;-mannosides.
+Only a single [[glycoside hydrolase]] of family [[GH113]] has been characterized, intracellular ''Aa''ManA from ''Alicyclobacillus acidocaldarius'' Tc-12-31 <cite>Zhang2008</cite>. This thermoacidophilic organism was originally selected for its ability to hydrolyse konjac glucomannan <cite>Zhang2008</cite>. The recombinantly-expressed enzyme possesses activity against polysaccharides containing &beta;-1,4-mannosidic linkages, including significant activity against konjac glucomannan, and galactomannan from locust bean gum. Some activity was also observed against crystalline ivory nut mannan (an unsubstituted &beta;-1,4-mannan) and guar gum (a more highly-substituted galactomannan) <cite>Zhang2008</cite>. No activity was observed against the other polysaccharides and ''p''-nitrophenyl glycosides tested, including ''p''-nitrophenyl &beta;- and &alpha;-mannosides.
 == 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]]s: ^^^Rohan Williams^^^ and ^^^Spencer Williams^^^
 * [[Responsible Curator]]: ^^^Spencer Williams^^^

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 == Three-dimensional structures ==
-The three dimensional structure was first reported for ''Aa''ManA, which possesses a classical (&beta;/&alpha;)<sub>8</sub> TIM barrel fold that aligns well with enzymes of family [[GH5]] <cite>Zhang2008</cite>. Alignment of the ‘’Aa’’ManA structure with Cel5G from ''Pseudoalteromonas haloplanktis'' revealed eight equivalent residues around the proposed active site pocket: Lys93, Thr95, Cys150, Glu151, Ser201, Tyr203, Glu231, and Trp281 <cite>Zhang2008</cite>.  Binary complexes of ''Aa''ManA with &beta;-mannosyl-1,4-mannoimidazole or &beta;-mannosyl-1,4-isofagomine support the identity of the active site residues originally proposed on the basis of structural comparisons of ''Aa''ManA with Cel5G and mutagenesis <cite>Williams2014</cite>. An ''active-site spanning'' ternary complex of ''Aa''ManA with &beta;-mannosyl-1,4-isofagomine and 1,4-&beta;-mannobiose has provided structural details of amino acids defining the -2 to +2 subsites <cite>Williams2014</cite>.
+The three dimensional structure was first reported for ''Aa''ManA, which possesses a classical (&beta;/&alpha;)<sub>8</sub> TIM barrel fold that aligns well with enzymes of family [[GH5]] <cite>Zhang2008</cite>. Alignment of the ''Aa''ManA structure with Cel5G from ''Pseudoalteromonas haloplanktis'' revealed eight equivalent residues around the proposed active site pocket: Lys93, Thr95, Cys150, Glu151, Ser201, Tyr203, Glu231, and Trp281 <cite>Zhang2008</cite>.  Binary complexes of ''Aa''ManA with &beta;-mannosyl-1,4-mannoimidazole or &beta;-mannosyl-1,4-isofagomine support the identity of the active site residues originally proposed on the basis of structural comparisons of ''Aa''ManA with Cel5G and mutagenesis <cite>Williams2014</cite>. An ''active-site spanning'' ternary complex of ''Aa''ManA with &beta;-mannosyl-1,4-isofagomine and 1,4-&beta;-mannobiose has provided structural details of amino acids defining the -2 to +2 subsites <cite>Williams2014</cite>.
 == Family Firsts ==

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 == Kinetics and Mechanism ==
-Thin layer chromatographic analysis of the hydrolysis products of ''Aa''ManA from ''A. acidocaldarius'' indicated ''[[endo]]''-type cleavage <cite>Zhang2008</cite>. The products also displayed obvious signs of [[transglycosylases|transglycosylation]], and thus ''Aa''ManA was assigned a [[retaining]] mechanism. The distance between the acid/base and nucleophile residues (assigned on the basis of structural comparison and mutagenesis, see below) is 4.75 Å <cite>Zhang2008</cite>. Together, these data support a [[classical Koshland retaining mechanism]]. Kinetic analysis of mannooligosaccharides reveals a preference for pentamannosides and higher; a tetramannoside was hydrolysed with ''k''<sub>cat</sub>/''K''<sub>M</sub> value approximately one quarter of that seen for the higher oligomers. Crystallographic evidence from a binary complexes of ''Aa''ManA with &beta;-mannosyl-1,4-mannoimidazole supports a <sup>1</sup>''S''<sub>5</sub>&rarr;''B''<sub>2,5</sub><sup>‡</sup>&rarr;<sup>O</sup>''S''<sub>2</sub> conformational reaction coordinate<cite>Williams2014</cite>.
+Thin layer chromatographic analysis of the hydrolysis products of ''Aa''ManA from ''A. acidocaldarius'' indicated ''[[endo]]''-type cleavage <cite>Zhang2008</cite>. The products also displayed obvious signs of [[transglycosylases|transglycosylation]], and thus ''Aa''ManA was assigned a [[retaining]] mechanism. The distance between the acid/base and nucleophile residues (assigned on the basis of structural comparison and mutagenesis, see below) is 4.75 Å <cite>Zhang2008</cite>. Together, these data support a [[classical Koshland retaining mechanism]]. Kinetic analysis of mannooligosaccharides reveals a preference for pentamannosides and higher; a tetramannoside was hydrolysed with ''k''<sub>cat</sub>/''K''<sub>M</sub> value approximately one quarter of that seen for the higher oligomers. Crystallographic evidence from a binary complexes of ''Aa''ManA with &beta;-mannosyl-1,4-mannoimidazole supports a <sup>1</sup>''S''<sub>5</sub>&rarr;''B''<sub>2,5</sub><sup>‡</sup>&rarr;<sup>O</sup>''S''<sub>2</sub> conformational reaction coordinate <cite>Williams2014</cite>.
 == Catalytic Residues ==

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 <biblio>
 #Zhang2008 pmid=18755688
-#Williams2014 pmid=
+#Williams2014 pmid=24339341
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH113]]

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 == Catalytic Residues ==
-Structural comparision of ''Aa''ManA with [[GH5]] endoglycosidases demonstrated conserved spatial arrangement of key active site amino acid residues <cite>Zhang2008</cite>. Structural comparison with Cel5G from ''Pseudoalteromonas haloplanktis'' suggested Glu151 to be the [[general acid/base]] and Glu231 to be the [[catalytic nucleophile]]. The Glu151Ala and Glu231Ala mutants did not affect overall fold but each resulted in a loss of approximately 1000-fold activity against mannan substrates, consistent with the proposed roles. Crystallographic studies with ‘’Aa’’ManA in complex with &beta;-mannosyl-1,4-mannoimidazole support the assignment of Glu151 as the acid/base <cite>Williams2014</cite>. A complex of ''Aa''ManA with &beta;-mannosyl-1,4-isofagomine supports the assignment of Glu231 as the nucleophile <cite>Williams2014</cite>. Crystallographic evidence from a binary complexes of ''Aa''ManA with &beta;-mannosyl-1,4-mannoimidazole supports a <sup>1</sup>''S''<sub>5</sub>&rarr;''B''<sub>2,5</sub><sup>‡</sup>&rarr;<sup>O</sup>''S''<sub>2</sub> conformational reaction coordinate <cite>Williams2014</cite>.
+Structural comparision of ''Aa''ManA with [[GH5]] endoglycosidases demonstrated conserved spatial arrangement of key active site amino acid residues <cite>Zhang2008</cite>. Structural comparison with Cel5G from ''Pseudoalteromonas haloplanktis'' suggested Glu151 to be the [[general acid/base]] and Glu231 to be the [[catalytic nucleophile]]. The Glu151Ala and Glu231Ala mutants did not affect overall fold but each resulted in a loss of approximately 1000-fold activity against mannan substrates, consistent with the proposed roles. Crystallographic studies with ''Aa''ManA in complex with &beta;-mannosyl-1,4-mannoimidazole support the assignment of Glu151 as the acid/base <cite>Williams2014</cite>. A complex of ''Aa''ManA with &beta;-mannosyl-1,4-isofagomine supports the assignment of Glu231 as the nucleophile <cite>Williams2014</cite>. Crystallographic evidence from a binary complexes of ''Aa''ManA with &beta;-mannosyl-1,4-mannoimidazole supports a <sup>1</sup>''S''<sub>5</sub>&rarr;''B''<sub>2,5</sub><sup>‡</sup>&rarr;<sup>O</sup>''S''<sub>2</sub> conformational reaction coordinate <cite>Williams2014</cite>.
 == Three-dimensional structures ==