Glycoside Hydrolase Family 85 - Revision history

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

2021-12-18T21:19:31Z

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

Spencer Williams: /* Catalytic Residues */

2013-06-27T05:47:55Z

Catalytic Residues

Harry Brumer: updated CAZyDBlink

2012-09-10T16:43:53Z

updated CAZyDBlink

Spencer Williams at 03:14, 14 June 2011

2011-06-14T03:14:46Z

Harry Brumer: /* Family Firsts */ fixed definition list formatting

2011-02-08T18:14:37Z

Family Firsts: fixed definition list formatting

Wade Abbott at 18:05, 8 February 2011

2011-02-08T18:05:09Z

Wade Abbott at 17:56, 8 February 2011

2011-02-08T17:56:01Z

Wade Abbott at 17:54, 8 February 2011

2011-02-08T17:54:00Z

Wade Abbott at 17:30, 8 February 2011

2011-02-08T17:30:40Z

Wade Abbott at 17:17, 8 February 2011

2011-02-08T17:17:26Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Wade Abbott^^^
+* [[Author]]: [[User:Wade Abbott|Wade Abbott]]
-* [[Responsible Curator]]:  ^^^Al Boraston^^^
+* [[Responsible Curator]]:  [[User:Al Boraston|Al Boraston]]
 ----

@@ Line 34: / Line 34: @@
 == Catalytic Residues ==
-Exploiting the [[transglycosylation]] capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>, which is a conserved role with E173 of Endo-A <cite>#14</cite>.
+Exploiting the [[transglycosylases|transglycosylase]] capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>, which is a conserved role with E173 of Endo-A <cite>#14</cite>.
 == Family Firsts ==

@@ Line 21: / Line 21: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH85.html
+| colspan="2" |{{CAZyDBlink}}GH85.html
 |}
 </div>

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Endo]]-beta-N-acetylglucosaminidases (ENGse) are [[glycoside hydrolase]]s that cleave the chitobiose core (GlcNAc-beta-1,4-GlcNac) of N-linked glycans.  Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.
+[[Endo]]-&beta;-N-acetylglucosaminidases (ENGse) are [[glycoside hydrolase]]s that cleave the chitobiose core (GlcNAc-&beta;-1,4-GlcNac) of N-linked glycans.  Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.
 == Kinetics and Mechanism ==
@@ Line 37: / Line 37: @@
 == Family Firsts ==
-;'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.
+;'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-&beta;-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.
 ;'''First [[catalytic nucleophile]] identification''': It was suggested that the 2-acetamido group acts as a substrate-borne nucleophile based on transglycosylation observed with a disaccharide oxazoline substrate <cite>#13</cite> .

@@ Line 37: / Line 37: @@
 == Family Firsts ==
-'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.
+;'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.
-'''First [[catalytic nucleophile]] identification''': It was suggested that the 2-acetamido group acts as a substrate-borne nucleophile based on transglycosylation observed with a disaccharide oxazoline substrate <cite>#13</cite> .
+;'''First [[catalytic nucleophile]] identification''': It was suggested that the 2-acetamido group acts as a substrate-borne nucleophile based on transglycosylation observed with a disaccharide oxazoline substrate <cite>#13</cite> .
-'''First [[general acid/base]] residue identification''': The residue that protonates the glycosidic oxygen and activates the incoming water was identified by the site-directed mutagenesis and azide/sodium formate rescue of E173 in Endo-A <cite>#14</cite>; and confirmed by the structure of Endo-D (E337) in complex with NAG-thiazoline <cite>#5</cite>.
+;'''First [[general acid/base]] residue identification''': The residue that protonates the glycosidic oxygen and activates the incoming water was identified by the site-directed mutagenesis and azide/sodium formate rescue of E173 in Endo-A <cite>#14</cite>; and confirmed by the structure of Endo-D (E337) in complex with NAG-thiazoline <cite>#5</cite>.
-'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: [{{PDBlink}}2w91 2w91] and [{{PDBlink}}2w92 2w92] (release date: 2009-01-27)<cite>#5</cite>.
+;'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: [{{PDBlink}}2w91 2w91] and [{{PDBlink}}2w92 2w92] (release date: 2009-01-27)<cite>#5</cite>.
 == References ==

@@ Line 41: / Line 41: @@
 '''First [[catalytic nucleophile]] identification''': It was suggested that the 2-acetamido group acts as a substrate-borne nucleophile based on transglycosylation observed with a disaccharide oxazoline substrate <cite>#13</cite> .
-'''First [[general acid/base]] residue identification''': The residue that protonates the glycosidic oxygen and activates the catatlytic water was identified by the site-directed mutagenesis and azide/sodium formate rescue of E173 in Endo-A <cite>#14</cite>; and confirmed by the structure of Endo-D in complex with NAG-thiazoline <cite>#5</cite>.
+'''First [[general acid/base]] residue identification''': The residue that protonates the glycosidic oxygen and activates the catalytic water was identified by the site-directed mutagenesis and azide/sodium formate rescue of E173 in Endo-A <cite>#14</cite>; and confirmed by the structure of Endo-D in complex with NAG-thiazoline <cite>#5</cite>.
 '''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: [{{PDBlink}}2w91 2w91] and [{{PDBlink}}2w92 2w92] (release date: 2009-01-27)<cite>#5</cite>.

@@ Line 31: / Line 31: @@
 == Kinetics and Mechanism ==
-Enzymes of family GH85 are [[retaining]] enzymes and are proposed to utilize [[neighboring group participation]] in a mechanism involving substrate-assisted catalysis by the 2-acetamido group of the sugar. This mechanism was proposed on the basis of the identification of a highly conserved catatlytic acid-base in Endo-A <cite>#14</cite> and transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was used to monitor the Endo-D catalyzed cleavage of a synthetic aryl glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in [[Glycoside Hydrolase Family 18]] and [[Glycoside Hydrolase Family 56]] <cite>#5</cite>.
+Enzymes of family GH85 are [[retaining]] enzymes and are proposed to utilize [[neighboring group participation]] in a mechanism involving substrate-assisted catalysis by the 2-acetamido group of the sugar. This mechanism was proposed on the basis of the identification of a highly conserved catatlytic acid-base E173 in Endo-A <cite>#14</cite> and transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was used to monitor the Endo-D catalyzed cleavage of a synthetic aryl glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in [[Glycoside Hydrolase Family 18]] and [[Glycoside Hydrolase Family 56]] <cite>#5</cite>.
 == Catalytic Residues ==

@@ Line 31: / Line 31: @@
 == Kinetics and Mechanism ==
-Enzymes of family GH85 are [[retaining]] enzymes and are proposed to utilize [[neighboring group participation]] in a mechanism involving substrate-assisted catalysis by the 2-acetamido group of the sugar. This mechanism was proposed on the basis of transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was used to monitor the Endo-D catalyzed cleavage of a synthetic aryl glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in [[Glycoside Hydrolase Family 18]] and [[Glycoside Hydrolase Family 56]] <cite>#5</cite>.
+Enzymes of family GH85 are [[retaining]] enzymes and are proposed to utilize [[neighboring group participation]] in a mechanism involving substrate-assisted catalysis by the 2-acetamido group of the sugar. This mechanism was proposed on the basis of the identification of a highly conserved catatlytic acid-base in Endo-A <cite>#14</cite> and transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was used to monitor the Endo-D catalyzed cleavage of a synthetic aryl glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in [[Glycoside Hydrolase Family 18]] and [[Glycoside Hydrolase Family 56]] <cite>#5</cite>.
 == Catalytic Residues ==
-Exploiting the [[transglycosylation]] capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>.
+Exploiting the [[transglycosylation]] capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>, which is a conserved role with E173 of Endo-A <cite>#14</cite>.
 == Family Firsts ==
@@ Line 41: / Line 41: @@
 '''First [[catalytic nucleophile]] identification''': It was suggested that the 2-acetamido group acts as a substrate-borne nucleophile based on transglycosylation observed with a disaccharide oxazoline substrate <cite>#13</cite> .
-'''First [[general acid/base]] residue identification''': The [[general base]] residue that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis of N175 in Endo-M  <cite>#10</cite>.
+'''First [[general acid/base]] residue identification''': The [[general base]] residue that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis and azide/sodium formate rescue of N173 in Endo-A <cite>#14</cite>.
 '''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: [{{PDBlink}}2w91 2w91] and [{{PDBlink}}2w92 2w92] (release date: 2009-01-27). <cite>#5</cite>.
@@ Line 60: / Line 60: @@
 #12 pmid=19327363
 #13 pmid=11514092
 </biblio>
 <!-- ATTN CURATOR: Please delete the "<nowiki>" and "</nowiki>" tags below when you are ready for the page to be included in the "GH Families" category, which is linked on the Main Page; ALSO: REPLACE "nnn" with the family number) -->
 [[Category:Glycoside Hydrolase Families|GH085]]