Glycoside Hydrolase Family 135 - Revision history

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

2021-12-18T21:20:28Z

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

Spencer Williams: Reverted edits by Spencer Williams (talk) to last revision by Harry Brumer

2016-11-25T03:35:52Z

Reverted edits by Spencer Williams (talk) to last revision by Harry Brumer

Spencer Williams at 03:35, 25 November 2016

2016-11-25T03:35:43Z

Harry Brumer at 19:57, 22 November 2016

2016-11-22T19:57:53Z

Harry Brumer: /* Family Firsts */ Fixed Spencer's poorly constructed link code

2016-11-03T21:39:32Z

Family Firsts: Fixed Spencer's poorly constructed link code

Spencer Williams at 21:27, 3 November 2016

2016-11-03T21:27:25Z

Spencer Williams at 02:14, 1 November 2016

2016-11-01T02:14:53Z

Harry Brumer: /* Three-dimensional structures */

2016-10-31T19:13:07Z

Three-dimensional structures

Harry Brumer at 19:12, 31 October 2016

2016-10-31T19:12:34Z

Harry Brumer: /* Substrate specificities */

2016-10-31T19:11:08Z

Substrate specificities

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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]]: ^^^Spencer Williams^^^
+* [[Author]]: [[User:Spencer Williams|Spencer Williams]]
-* [[Responsible Curator]]:  ^^^Spencer Williams^^^
+* [[Responsible Curator]]:  [[User:Spencer Williams|Spencer Williams]]
 ----

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 ;First catalytic nucleophile identification: Currently unknown.
 ;First general acid/base residue identification: Currently unknown.
-;First 3-D structure: Sph3 from ''Aspergillus clavatus'' (PDB ID [{{PDBlink}}3vsv 3vsv]) <cite>Bamford2015</cite>.
+;First 3-D structure: Sph3 from ''Aspergillus clavatus'' (PDB ID [{{PDBlink}}5d6t 5d6t]) <cite>Bamford2015</cite>.
 == References ==

@@ Line 45: / Line 45: @@
 ;First catalytic nucleophile identification: Currently unknown.
 ;First general acid/base residue identification: Currently unknown.
-;First 3-D structure: Sph3 from ''Aspergillus clavatus'' (PDB ID [{{PDBlink}}5d6t 5d6t]) <cite>Bamford2015</cite>.
+;First 3-D structure: Sph3 from ''Aspergillus clavatus'' (PDB ID [{{PDBlink}}3vsv 3vsv]) <cite>Bamford2015</cite>.
 == References ==

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 == Family Firsts ==
-;First stereochemistry determination: Unknown.
+;First stereochemistry determination: Currently unknown.
-;First catalytic nucleophile identification: Unknown.
+;First catalytic nucleophile identification: Currently unknown.
-;First general acid/base residue identification: Unknown.
+;First general acid/base residue identification: Currently unknown.
 ;First 3-D structure: Sph3 from ''Aspergillus clavatus'' (PDB ID [{{PDBlink}}5d6t 5d6t]) <cite>Bamford2015</cite>.

@@ Line 45: / Line 45: @@
 ;First catalytic nucleophile identification: Unknown.
 ;First general acid/base residue identification: Unknown.
-;First 3-D structure: Sph3 from ''Aspergillus clavatus'' PDB code [{{PDBlink}}5d6t] <cite>Bamford2015</cite>.
+;First 3-D structure: Sph3 from ''Aspergillus clavatus'' (PDB ID [{{PDBlink}}5d6t 5d6t]) <cite>Bamford2015</cite>.
 == References ==

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 == Substrate specificities ==
-A single report has disclosed fungal [[glycoside hydrolases]] with the ability to degrade the fungal heteropolysaccharide galactosaminogalactan (GAG; not to be confused with glycosaminoglycan mucopolysaccharides) <cite>Bamford2015</cite>. Galactosaminogalactan is produced by ''Aspergillus fumigatus'' as a linear heterogeneous exopolysaccharide composed of &alpha;-1,4-linked galactose, ''N''-acetylgalactosamine, and galactosamine residues. GAG is found in both a secreted form and bound to the cell wall of hyphae <cite>Fontaine2011</cite>. A recombinant ''Aspergillus clavatus'' protein from GH135 was demonstrated to hydrolyze both purified and cell wall-associated GAG. While it is unclear precisely where within the GAG chain the enzyme acts [and thus whether it should be considered an &alpha;-galactosidase, &alpha;-galactosaminase (i.e. cleaving an &alpha;-galactosamine linkage, e.g. [[GH113]]), or an ''N''-acetyl-&alpha;-galactosaminidase], a three-dimensional complex with ''N''-acetylgalactosamine (see below) suggests that the enzyme possesses &alpha;-galactosaminidase activity. The majority of genes encoding family 135 members are found in fungi, with smaller numbers in bacteria and archaea.
+A single report has disclosed fungal [[glycoside hydrolases]] with the ability to degrade the fungal heteropolysaccharide galactosaminogalactan (GAG; not to be confused with glycosaminoglycan mucopolysaccharides) <cite>Bamford2015</cite>. Galactosaminogalactan is produced by ''Aspergillus fumigatus'' as a linear heterogeneous exopolysaccharide composed of &alpha;-1,4-linked galactose, ''N''-acetylgalactosamine, and galactosamine residues. GAG is found in both a secreted form and bound to the cell wall of hyphae <cite>Fontaine2011</cite>. A recombinant ''Aspergillus clavatus'' protein from GH135 was demonstrated to hydrolyze both purified and cell wall-associated GAG. While it is unclear precisely where within the GAG chain the enzyme acts [and thus whether it should be considered an &alpha;-galactosidase, &alpha;-galactosaminase (i.e. cleaving an &alpha;-galactosamine linkage, e.g. [[GH113]]), or an ''N''-acetyl-&alpha;-galactosaminidase], a three-dimensional complex with ''N''-acetylgalactosamine (see below) suggests that the enzyme possesses ''N''-acetyl-&alpha;-galactosaminidase activity. The majority of genes encoding family 135 members are found in fungi, with smaller numbers in bacteria and archaea.
 == Kinetics and Mechanism ==

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 == Three-dimensional structures ==
-Three-dimensional structures are available for ''Aspergillus clavatus'' Sph3 <cite>Bamford2015</cite>. These structures reveal that the protein has a classical (&beta;/&alpha;)<sub>8</sub> TIM barrel fold, with two small additional helices, one on either end of the sixth &alpha; helix. This fold was described as sharing similarities with enzymes belonging to families [[GH18]], [[GH27]], and [[GH84]]. The putative active site was identified through the acquisition of a binary complex of Sph3 with ''N''-acetylgalactosamine. The proposed cleft is lined with highly conserved tyrosine residues and three acidic residues: Asp166, Glu167, and Glu222. In the Sph3-GalNAc complex, the ''N ''-acetyl group forms hydrogen bonds with Glu222 and Tyr65. Glu222 is coordinated by Asn202, which in turn hydrogen bonds to Asp166. A hydrogen bond network through a bridging water molecule connects Glu167, Asp166, and the galactopyranose ring oxygen.
+Three-dimensional structures are available for ''Aspergillus clavatus'' Sph3 <cite>Bamford2015</cite>. These structures reveal that the protein has a classical (&beta;/&alpha;)<sub>8</sub> TIM barrel fold, with two small additional helices, one on either end of the sixth &alpha; helix. This fold was described as sharing similarities with enzymes belonging to families [[GH18]], [[GH27]], and [[GH84]]. The putative active site was identified through the acquisition of a binary complex of Sph3 with ''N''-acetylgalactosamine. The proposed cleft is lined with highly conserved tyrosine residues and three acidic residues: Asp166, Glu167, and Glu222. In the Sph3-GalNAc complex, the ''N''-acetyl group forms hydrogen bonds with Glu222 and Tyr65. Glu222 is coordinated by Asn202, which in turn hydrogen bonds to Asp166. A hydrogen bond network through a bridging water molecule connects Glu167, Asp166, and the galactopyranose ring oxygen.
 == Family Firsts ==

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 == Catalytic Residues ==
-Structural and sequence alignments identified three conserved acidic amino acid residues, Asp166, Glu167, and Glu222 (numbering for ''Aspergillus clavatus''), which were located within the putative active site groove. Mutagenesis of these residues individually either decreased or abolished the catalytic activity of Sph3 towards purified GAG. The D166A, D166N, and E167A variants displayed no significant activity. The E222A variant displayed no activity, while the E222Q variant retained 60% of wild-type activity.
+Structural and sequence alignments identified three conserved acidic amino acid residues, Asp166, Glu167, and Glu222 (numbering for ''Aspergillus clavatus'' Sph3 <cite>Bamford2015</cite>), which were located within the putative active site groove. Mutagenesis of these residues individually either decreased or abolished the catalytic activity of Sph3 towards purified galactosaminogalactan. The D166A, D166N, and E167A variants displayed no significant activity. The E222A variant displayed no activity, while the E222Q variant retained 60% of wild-type activity.
 == Three-dimensional structures ==