Glycoside Hydrolase Family 114 - Revision history

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

2021-12-18T21:20:50Z

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

Spencer Williams at 03:27, 17 September 2019

2019-09-17T03:27:29Z

Spencer Williams at 03:26, 17 September 2019

2019-09-17T03:26:55Z

Spencer Williams: /* Three-dimensional structures */

2019-09-17T03:22:55Z

Three-dimensional structures

Spencer Williams: /* Catalytic Residues */

2019-09-17T03:16:59Z

Catalytic Residues

Spencer Williams: /* Three-dimensional structures */

2019-09-17T03:14:42Z

Three-dimensional structures

Spencer Williams: /* Substrate specificities */

2019-09-17T03:14:10Z

Substrate specificities

Spencer Williams at 12:06, 15 September 2019

2019-09-15T12:06:10Z

Spencer Williams at 11:55, 15 September 2019

2019-09-15T11:55:05Z

Harry Brumer: /* References */

2016-09-06T22:00:37Z

References

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

@@ Line 17: / Line 17: @@
 |-
 |'''Active site residues'''
-|not known
+|known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''

@@ Line 31: / Line 31: @@
 == Kinetics and Mechanism ==
-The ''endo''-α-1,4-polygalactosaminidase from ''Pseudomonas'' sp. 881 possesses activity on deacetylated α-1,4-polygalactosamine, but has no activity on fully ''N''-acetylated α-1,4-polygalactosamine <cite>#Tamura1988</cite>. Tetraose and longer galactosamine oligosaccharides are hydrolyzed to galactosaminobiose and galactosaminotriose as the final products <cite>Tamura1992</cite>. Based on the dependence of rate on the chain length of the substrate, it was proposed that the enzyme has 8 subsites <cite>Tamura1992</cite>. The enzyme is inhibited by metal ions including Hg<sup>2+</sup>, Fe<sup>2+</sup> and Sn<sup>2+</sup> <cite>#Tamura1988</cite>. Digest of galactosaminotetraose resulted in the transient formation of galactosaminohexaose through a transglycosylation reaction <cite>Tamura1992</cite>. This supports the assignment of a [[retaining]] mechanism to this enzyme and family, and is consistent with the enzyme utilizing a [[classical Koshland double-displacement mechanism]].
+The ''endo''-α-1,4-polygalactosaminidase from ''Pseudomonas'' sp. 881 possesses activity on deacetylated α-1,4-polygalactosamine, but has no activity on fully ''N''-acetylated α-1,4-polygalactosamine <cite>#Tamura1988</cite>. Similar trends were seen for Ega3 <cite>Bamford2019</cite>. Tetraose and longer galactosamine oligosaccharides are hydrolyzed to galactosaminobiose and galactosaminotriose as the final products <cite>Tamura1992 bamford2019</cite>. Based on the dependence of rate on the chain length of the substrate, it was proposed that the ''Pseudomonas'' enzyme has 8 subsites <cite>Tamura1992</cite>. The enzyme is inhibited by metal ions including Hg<sup>2+</sup>, Fe<sup>2+</sup> and Sn<sup>2+</sup> <cite>#Tamura1988</cite>. Digest of galactosaminotetraose resulted in the transient formation of galactosaminohexaose through a transglycosylation reaction <cite>Tamura1992</cite>. This supports the assignment of a [[retaining]] mechanism to this enzyme and family, and is consistent with the enzyme utilizing a [[classical Koshland double-displacement mechanism]].
 == Catalytic Residues ==
@@ Line 37: / Line 37: @@
 == Three-dimensional structures ==
-The 3D crystal structure of Ega3 revealed a modified (β/α)<sub>8</sub>-barrel that lacks β-strand 5 and α-helices 1 and 8. A structural insertion after β-strand 3 creates a deep cleft where galactosamine bound. Ega3 shared 3-D similarity with the family [[GH166]] endo-α-1,4-N-acetylgalactosaminidase Pel<sub>h</sub>. In silico docking of α-1,4-(GalN)<sub>5</sub> revealed six substrate binding subsites.
+The 3D crystal structure of Ega3 revealed a modified (β/α)<sub>8</sub>-barrel that lacks β-strand 5 and α-helices 1 and 8 <cite>Bamford2019</cite>. A structural insertion after β-strand 3 creates a deep cleft where galactosamine bound. Ega3 shared 3-D similarity with the family [[GH166]] endo-α-1,4-N-acetylgalactosaminidase Pel<sub>h</sub>. In silico docking of α-1,4-(GalN)<sub>5</sub> revealed six substrate binding subsites.
 == Family Firsts ==

@@ Line 37: / Line 37: @@
 == Three-dimensional structures ==
-The 3D crystal structure of Ega3 revealed a modified (β/α)<sub>8</sub>-barrel that lacks β-strand 5 and α-helices 1 and 8. A structural insertion after β-strand 3 creates a deep cleft where galactosamine bound.
+The 3D crystal structure of Ega3 revealed a modified (β/α)<sub>8</sub>-barrel that lacks β-strand 5 and α-helices 1 and 8. A structural insertion after β-strand 3 creates a deep cleft where galactosamine bound. Ega3 shared 3-D similarity with the family [[GH166]] endo-α-1,4-N-acetylgalactosaminidase Pel<sub>h</sub>. In silico docking of α-1,4-(GalN)<sub>5</sub> revealed six substrate binding subsites.
 == Family Firsts ==

@@ Line 34: / Line 34: @@
 == Catalytic Residues ==
-The 3D structure of Ega3 revealed two candidate active site residues: Asp189 and Glu247 <cite>Bamford2019</cite>. Mutagenesis supports their role as essential catalytic residues. Docking studies of an oligosaccharide led to the proposal that Asp189 is the catalytic nucleophile and Glu247 is the general acid/base, in a [[classical Koshland retaining mechanism]] <cite>Bamford2019</cite>.
+The 3D structure of the catalytic domain of Ega3 revealed two candidate active site residues: Asp189 and Glu247 <cite>Bamford2019</cite>. Mutagenesis supports their role as essential catalytic residues. Docking studies of an oligosaccharide led to the proposal that Asp189 is the catalytic nucleophile and Glu247 is the general acid/base, in a [[classical Koshland retaining mechanism]] <cite>Bamford2019</cite>.
 == Three-dimensional structures ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-Enzymes of [[glycoside hydrolase]] family 114 are ''endo''-α-1,4-polygalactosaminidases. Examples include the foundation member of this family from ''Pseudomonas'' sp. 881 <cite>Tamura1995</cite> and Ega3 from ''Aspergillus fumigatus'' <cite>Bamford2019</cite>. This enzyme hydrolyzes α-1,4-polygalactosamine to oligosaccharides in an [[endo]]-acting manner. α-1,4-Polygalactosamine, also known as galactosaminoglycan, is a polymer consisting of α-1,4-linked galactosamine residues, which is only partially ''N''-acetylated, and may also contain ''N''-formyl residues.  The polysaccharide is biosynthesized by fungi including ''Aspergillus parasiticus'' <cite>Distiller1960</cite> and ''Paecilomyces'' sp. I-1 <cite>Takagi1985</cite>. An endogalactosaminidase has been purified from ''Streptomyces griseus''; the sequence of this protein is unknown <cite>Riessig1975</cite>.
+Enzymes of [[glycoside hydrolase]] family 114 are ''endo''-α-1,4-polygalactosaminidases. Examples include the foundation member of this family from ''Pseudomonas'' sp. 881 <cite>Tamura1995</cite> and Ega3 from ''Aspergillus fumigatus'' <cite>Bamford2019</cite>. These enzymes hydrolyze α-1,4-polygalactosamine to oligosaccharides in an [[endo]]-acting manner. α-1,4-Polygalactosamine, also known as galactosaminoglycan, is a polymer consisting of α-1,4-linked galactosamine residues, which is only partially ''N''-acetylated, and may also contain ''N''-formyl residues.  The polysaccharide is biosynthesized by fungi including ''Aspergillus parasiticus'' <cite>Distiller1960</cite> and ''Paecilomyces'' sp. I-1 <cite>Takagi1985</cite>. An endogalactosaminidase has been purified from ''Streptomyces griseus''; the sequence of this protein is unknown <cite>Riessig1975</cite>.
 == Kinetics and Mechanism ==

@@ Line 34: / Line 34: @@
 == Catalytic Residues ==
-None known.
+The 3D structure of Ega3 revealed two candidate active site residues: Asp189 and Glu247 <cite>Bamford2019</cite>. Mutagenesis supports their role as essential catalytic residues. Docking studies of an oligosaccharide led to the proposal that Asp189 is the catalytic nucleophile and Glu247 is the general acid/base, in a [[classical Koshland retaining mechanism]] <cite>Bamford2019</cite>.
 == Three-dimensional structures ==
-No 3-D structure has been reported for any member of this family.
+The 3D crystal structure of Ega3 revealed a modified (β/α)8-barrel that lacks β-strand 5 and α-helices 1 and 8. A structural insertion after β-strand 3 creates a deep cleft where galactosamine bound.
 == Family Firsts ==
 ;First stereochemistry determination: A retaining mechanism may be inferred from report of transglycosylation activity <cite>Tamura1992</cite>.
-;First catalytic nucleophile identification: Not known.
+;First catalytic nucleophile identification: Asp189 in Ega3 is proposed to be the catalytic nucleophile <cite>Bamford2019</cite>.
-;First general acid/base residue identification: Not known.
+;First general acid/base residue identification: Glu247 in Ega3 is proposed to be the catalytic nucleophile <cite>Bamford2019</cite>.
-;First 3-D structure: None reported.
+;First 3-D structure: Ega3 from ''Aspergillus fumigatus'' <cite>Bamford2019</cite>.
 == References ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-Only a single enzyme of [[glycoside hydrolase]] family 114 has been characterized; an ''endo''-α-1,4-polygalactosaminidase from ''Pseudomonas'' sp. 881 <cite>Tamura1995</cite>. This enzyme hydrolyzes α-1,4-polygalactosamine to oligosaccharides in an [[endo]]-acting manner. α-1,4-Polygalactosamine, also known as galactosaminoglycan, is a polymer consisting of α-1,4-linked galactosamine residues, which is only partially ''N''-acetylated, and may also contain ''N''-formyl residues.  The polysaccharide is biosynthesized by fungi including ''Aspergillus parasiticus'' <cite>Distiller1960</cite> and ''Paecilomyces'' sp. I-1 <cite>Takagi1985</cite>. An endogalactosaminidase has been purified from ''Streptomyces griseus''; the sequence of this protein is unknown <cite>Riessig1975</cite>.
+Enzymes of [[glycoside hydrolase]] family 114 are ''endo''-α-1,4-polygalactosaminidases. Examples include the foundation member of this family from ''Pseudomonas'' sp. 881 <cite>Tamura1995</cite> and Ega3 from ''Aspergillus fumigatus'' <cite>Bamford2019</cite>. This enzyme hydrolyzes α-1,4-polygalactosamine to oligosaccharides in an [[endo]]-acting manner. α-1,4-Polygalactosamine, also known as galactosaminoglycan, is a polymer consisting of α-1,4-linked galactosamine residues, which is only partially ''N''-acetylated, and may also contain ''N''-formyl residues.  The polysaccharide is biosynthesized by fungi including ''Aspergillus parasiticus'' <cite>Distiller1960</cite> and ''Paecilomyces'' sp. I-1 <cite>Takagi1985</cite>. An endogalactosaminidase has been purified from ''Streptomyces griseus''; the sequence of this protein is unknown <cite>Riessig1975</cite>.
 == Kinetics and Mechanism ==
@@ Line 53: / Line 53: @@
 #Distiller1960 pmid=13816939
 #Takagi1985 Takagi, H., Kadowaki, K. Purification and Chemical Properties of a Flocculant Produced by Paecilomyces. ''Agric. Biol. Chem.'' 1985, 49, 3159-3164. [http://dx.doi.org/10.1080/00021369.1985.10867250 DOI: 10.1080/00021369.1985.10867250]
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH114]]

@@ Line 50: / Line 50: @@
 #Tamura1992 pmid=27320986
 #Riessig1975 pmid=3271
-#Tamura1988 Tamura, J.-I., Takagi, H., Kadowaki, K. Purification and Some Properties of the Endo α-1,4 Polygalactosaminidase from Pseudomonas sp., ''Agric. Biol. Chem.'' 1988, 52 , 2475-2484. [http://dx.doi.org/10.1080/00021369.1988.10869068 DOI: 10.1080/00021369.1988.10869068].
+#Tamura1988 Tamura, J.-I., Takagi, H., Kadowaki, K. Purification and Some Properties of the Endo α-1,4 Polygalactosaminidase from Pseudomonas sp., ''Agric. Biol. Chem.'' 1988, 52, 2475-2484. [http://dx.doi.org/10.1080/00021369.1988.10869068 DOI: 10.1080/00021369.1988.10869068].
 #Distiller1960 pmid=13816939
 #Takagi1985 Takagi, H., Kadowaki, K. Purification and Chemical Properties of a Flocculant Produced by Paecilomyces. ''Agric. Biol. Chem.'' 1985, 49, 3159-3164. [http://dx.doi.org/10.1080/00021369.1985.10867250 DOI: 10.1080/00021369.1985.10867250]