Glycoside Hydrolase Family 129 - Revision history

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

2021-12-18T21:15:21Z

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

Harry Brumer: Added ^^^Mayo Sato^^^ as a co-author

2018-02-09T17:54:11Z

Added ^^^Mayo Sato^^^ as a co-author

Spencer Williams at 01:50, 26 November 2012

2012-11-26T01:50:26Z

Spencer Williams at 01:46, 26 November 2012

2012-11-26T01:46:54Z

Spencer Williams at 01:46, 26 November 2012

2012-11-26T01:46:31Z

Shinya Fushinobu at 11:30, 13 November 2012

2012-11-13T11:30:06Z

Harry Brumer: /* Catalytic Residues */

2012-11-12T20:29:13Z

Catalytic Residues

Harry Brumer: /* Catalytic Residues */

2012-11-12T20:28:10Z

Catalytic Residues

Harry Brumer: /* Catalytic Residues */ added links

2012-11-12T20:26:01Z

Catalytic Residues: added links

Harry Brumer: minor language editing, etc.

2012-11-12T17:40:16Z

minor language editing, etc.

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Hisashi Ashida^^^ and ^^^Mayo Sato^^^
+* [[Author]]: [[User:Hisashi Ashida|Hisashi Ashida]] and [[User:Mayo Sato|Mayo Sato]]
-* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
+* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 ----

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Hisashi Ashida^^^
+* [[Author]]: ^^^Hisashi Ashida^^^ and ^^^Mayo Sato^^^
 * [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
 ----

@@ Line 38: / Line 38: @@
 == Catalytic Residues ==
-Asp435 in NagBb is predicted as [[catalytic nucleophile]] by remote homology-based fold recognition using [[GH13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template <cite>Kiyohara2012a</cite>. Asp330 in NagBb may be the so-called "fixer": analogous to the third invariant actve-site residue conserved in [[GH101]] and [[GH13]] enzymes, which is proposed as a transition-state stabilizer.  The [[general acid/base]] residue in GH129 unknown.
+Asp435 in NagBb is predicted as [[catalytic nucleophile]] by remote homology-based fold recognition using [[GH13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template <cite>Kiyohara2012a</cite>. Asp330 in NagBb may be the so-called "fixer": analogous to the third invariant actve-site residue conserved in [[GH101]] and [[GH13]] enzymes, which is proposed as a [[transition state]] stabilizer.  The [[general acid/base]] residue in GH129 unknown.
 == Three-dimensional structures ==

@@ Line 45: / Line 45: @@
 == Family Firsts ==
 ;First stereochemistry determination: NagBb from ''Bifidobacterium bifidum'' JCM 1254 by normal-phase HPLC <cite>Kiyohara2012a</cite>.
-;First catalytic nucleophile identification: Predicted to be Asp435 in NagBb based on homology modelling <cite>Kiyohara2012a</cite>.
+;First [[catalytic nucleophile]] identification: Predicted to be Asp435 in NagBb based on homology modelling <cite>Kiyohara2012a</cite>.
-;First general acid/base residue identification: ''Not known.''
+;First [[general acid/base]] residue identification: ''Not known.''
 ;First 3-D structure: ''None.''

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-This family of glycoside hydrolases was established based on the &alpha;-''N''-acetylgalactosaminidase (NagBb) from ''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with  [[GH101]] endo-&alpha;-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>.
+This family of [[glycoside hydrolases]] was established based on the &alpha;-''N''-acetylgalactosaminidase (NagBb) from ''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with  [[GH101]] endo-&alpha;-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>.
 Before the establishment of this family, it has been predicted as a hypothetical glycoside hydrolase-like (GHL) family GHL1 <cite>Naumoff2010 Naumoff2011</cite>.
 NagBb acts more rapidly on GalNAc&alpha;1-''p''NP than Gal&beta;1-3GalNAc&alpha;1-''p''NP, therefore its substrate specificity is quite different from [[GH101]] enzymes (EC [{{EClink}}3.2.1.97 3.2.1.97]). This specificity is also different from those of previously known exo-&alpha;-''N''-acetylgalactosaminidases  (EC [{{EClink}}3.2.1.49 3.2.1.49]) in [[GH27]], [[GH36]] and [[GH109]]. As such, NagBb may be appropriately referred to as a exo/endo-&alpha;-''N''-acetylgalactosaminidase.
@@ Line 35: / Line 35: @@
 == Kinetics and Mechanism ==
-NagBb is a retaining enzyme. The stereochemistry of hydrolysis has been monitored by normal-phase HPLC using GalNAc&alpha;1-''p''NP as a substrate <cite>Kiyohara2012a</cite>. GH129 is distantly related to [[GH101]] as well as [[GH13]] &alpha;-amylases; members of these latter two families are also classified as retaining enzymes.
+NagBb is a [[retaining]] enzyme. The stereochemistry of hydrolysis has been monitored by normal-phase HPLC using GalNAc&alpha;1-''p''NP as a substrate <cite>Kiyohara2012a</cite>. GH129 is distantly related to [[GH101]] as well as [[GH13]] &alpha;-amylases; members of these latter two families are also classified as [[retaining]] enzymes.
 == Catalytic Residues ==
-Asp-435 in NagBb is predicted as [[catalytic nucleophile]] by remote homology-based fold recognition using [[GH13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template <cite>Kiyohara2012a</cite>. Asp-330 in NagBb may be the so-called "fixer": analogous to the third invariant actve-site residue conserved in [[GH101]] and [[GH13]] enzymes, which is proposed as a transition-state stabilizer.  The [[general acid/base]] residue is in GH129 unknown.
+Asp435 in NagBb is predicted as [[catalytic nucleophile]] by remote homology-based fold recognition using [[GH13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template <cite>Kiyohara2012a</cite>. Asp330 in NagBb may be the so-called "fixer": analogous to the third invariant actve-site residue conserved in [[GH101]] and [[GH13]] enzymes, which is proposed as a transition-state stabilizer.  The [[general acid/base]] residue in GH129 unknown.
 == Three-dimensional structures ==
@@ Line 45: / Line 45: @@
 == Family Firsts ==
 ;First stereochemistry determination: NagBb from ''Bifidobacterium bifidum'' JCM 1254 by normal-phase HPLC <cite>Kiyohara2012a</cite>.
-;First catalytic nucleophile identification: ''To be determined experimentally.''
+;First catalytic nucleophile identification: Predicted to be Asp435 in NagBb based on homology modelling <cite>Kiyohara2012a</cite>.
-;First general acid/base residue identification: ''To be determined experimentally.''
+;First general acid/base residue identification: ''Not known.''
-;First 3-D structure: ''To be determined experimentally.''
+;First 3-D structure: ''None.''
 == References ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-This family of glycoside hydrolases was established based on the &alpha;-''N''-acetylgalactosaminidase (NagBb) from
+This family of glycoside hydrolases was established based on the &alpha;-''N''-acetylgalactosaminidase (NagBb) from ''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with  [[GH101]] endo-&alpha;-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>.
-''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with  [[GH101]] endo-&alpha;-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>. NagBb acts more rapidly on GalNAc&alpha;1-''p''NP than Gal&beta;1-3GalNAc&alpha;1-''p''NP, therefore its substrate specificity is quite different from [[GH101]] enzymes (EC [{{EClink}}3.2.1.97 3.2.1.97]). This specificity is also different from those of previously known exo-&alpha;-''N''-acetylgalactosaminidases  (EC [{{EClink}}3.2.1.49 3.2.1.49]) in [[GH27]], [[GH36]] and [[GH109]]. As such, NagBb may be appropriately referred to as a exo/endo-&alpha;-''N''-acetylgalactosaminidase.
+Before the establishment of this family, it has been predicted as a hypothetical glycoside hydrolase-like (GHL) family GHL1 <cite>Naumoff2010 Naumoff2011</cite>.
 NagBb most preferably hydrolyzes GalNAc&alpha;1-Ser, a minimal structure of Tn antigen on mucin-type glycoproteins, suggesting that NagBb might be involved in degradation of intestinal mucins. The members of GH129 are distributed in several bifidobacterial species such as ''B. longum'' subsp. ''longum'', ''B. longum'' subsp. ''infants'' and ''B. breve'', which are frequently found in intestines of infants.
@@ Line 50: / Line 51: @@
 == References ==
 <biblio>
-#Kiyohara2012a pmid=22090027]
+#Kiyohara2012a pmid=22090027
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH129]]

@@ Line 37: / Line 37: @@
 == Catalytic Residues ==
-Asp-435 in NagBb is predicted as [[catalytic nucleophile]] by remote homology-based fold recognition using [[GH13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template <cite>Kiyohara2012a</cite>. Asp-330 in NagBb may be the so-called "fixer": the third invariant catalytic residue conserved in [[GH101]] and [[GH13]] enzymes.  The [[general acid/base]] residue is in GH129 unknown.
+Asp-435 in NagBb is predicted as [[catalytic nucleophile]] by remote homology-based fold recognition using [[GH13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template <cite>Kiyohara2012a</cite>. Asp-330 in NagBb may be the so-called "fixer": analogous to the third invariant catalytic residue conserved in [[GH101]] and [[GH13]] enzymes, which is proposed as a transition-state stabilizer.  The [[general acid/base]] residue is in GH129 unknown.
 == Three-dimensional structures ==