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Difference between revisions of "Glycoside Hydrolase Family 129"

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== Substrate specificities ==
 
== Substrate specificities ==
 
This family of glycoside hydrolases was recently established for NagBb from  
 
This family of glycoside hydrolases was recently established for NagBb from  
''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with GH101 endo-α-''N''-acetylgalactosaminidases. NagBb more rapidly act on GalNAcα1-''p''NP than Galβ1-3GalNAcα1-''p''NP; therefore its substrate specificity is quite different from GH101 enzymes (EC 3.2.1.97). It is also different from those of previously known exo-α-''N''-acetylgalactosaminidases (EC 3.2.1.49) in GH27, GH36 and GH109. Thus, NagBb should be called as exo/endo-α-''N''-acetylgalactosaminidase. NagBb most preferably hydrolyzes GalNAcα1-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.
+
''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with [[Glycoside Hydrolase Family 101]] endo-&alpha;-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>. NagBb more rapidly act on GalNAc&alpha;1-''p''NP than Gal&beta;1-3GalNAc&alpha;1-''p''NP; therefore its substrate specificity is quite different from [[Glycoside Hydrolase Family 101]] enzymes (EC [{{EClink}}3.2.1.97 3.2.1.97]). It is also different from those of previously known exo-&alpha;-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.49 3.2.1.49]) in [[Glycoside Hydrolase Family 27]], [[Glycoside Hydrolase Family 36]] and [[Glycoside Hydrolase Family 109]]. Thus, NagBb should be called as exo/endo-&alpha;-''N''-acetylgalactosaminidase. 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.
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
NagBb is a retaining enzyme. The stereochemistry of hydrolysis has been monitored by normal-phase HPLC using GalNAcα1-''p''NP as a substrate. GH129 is distantly related with GH101 as well as GH13 α-amylases; the latter two family members 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. GH129 is distantly related with [[Glycoside Hydrolase Family 101]] as well as [[Glycoside Hydrolase Family 13]] &alpha;-amylases; the latter two family members are also classified as retaining enzymes.
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
Asp-435 in NagBb is predicted as catalytic nucleophile by the remote homology-based fold recognition method using GH13 α-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code 1JI1) as a template. Asp-330 in NagBb may be "fixer", the third invariant catalytic residue conserved in GH101 and GH13 enzymes. General acid/base residue is unknown.
+
Asp-435 in NagBb is predicted as catalytic nucleophile by the remote homology-based fold recognition method using [[Glycoside Hydrolase Family 13]] &alpha;-amylase 1 (TVAI) from ''Thermoactinomyces vulgaris'' R-47 (PDB code [{{PDBlink}}1JI1 1JI1]) as a template. Asp-330 in NagBb may be "fixer", the third invariant catalytic residue conserved in [[Glycoside Hydrolase Family 101]] and [[Glycoside Hydrolase Family 13]] enzymes. General acid/base residue is unknown.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
Line 48: Line 48:
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#Cantarel2009 pmid=18838391
+
#Kiyohara2012a pmid=22090027
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
 
 
</biblio>
 
</biblio>
  
 
[[Category:Glycoside Hydrolase Families|GH129]]
 
[[Category:Glycoside Hydrolase Families|GH129]]

Revision as of 07:01, 7 March 2012

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Glycoside Hydrolase Family GH129
Clan GH-x
Mechanism retaining
Active site residues Asp
CAZy DB link
http://www.cazy.org/GH129.html


Substrate specificities

This family of glycoside hydrolases was recently established for NagBb from Bifidobacterium bifidum JCM 1254, which shows slight sequence similarity with Glycoside Hydrolase Family 101 endo-α-N-acetylgalactosaminidases [1]. NagBb more rapidly act on GalNAcα1-pNP than Galβ1-3GalNAcα1-pNP; therefore its substrate specificity is quite different from Glycoside Hydrolase Family 101 enzymes (EC 3.2.1.97). It is also different from those of previously known exo-α-N-acetylgalactosaminidases (EC 3.2.1.49) in Glycoside Hydrolase Family 27, Glycoside Hydrolase Family 36 and Glycoside Hydrolase Family 109. Thus, NagBb should be called as exo/endo-α-N-acetylgalactosaminidase. NagBb most preferably hydrolyzes GalNAcα1-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.

Kinetics and Mechanism

NagBb is a retaining enzyme. The stereochemistry of hydrolysis has been monitored by normal-phase HPLC using GalNAcα1-pNP as a substrate. GH129 is distantly related with Glycoside Hydrolase Family 101 as well as Glycoside Hydrolase Family 13 α-amylases; the latter two family members are also classified as retaining enzymes.

Catalytic Residues

Asp-435 in NagBb is predicted as catalytic nucleophile by the remote homology-based fold recognition method using Glycoside Hydrolase Family 13 α-amylase 1 (TVAI) from Thermoactinomyces vulgaris R-47 (PDB code 1JI1) as a template. Asp-330 in NagBb may be "fixer", the third invariant catalytic residue conserved in Glycoside Hydrolase Family 101 and Glycoside Hydrolase Family 13 enzymes. General acid/base residue is unknown.

Three-dimensional structures

Family Firsts

First stereochemistry determination
NagBb from Bifidobacterium bifidum JCM 1254 by normal-phase HPLC
First catalytic nucleophile identification
First general acid/base residue identification
First 3-D structure

References

  1. Kiyohara M, Nakatomi T, Kurihara S, Fushinobu S, Suzuki H, Tanaka T, Shoda SI, Kitaoka M, Katayama T, Yamamoto K, and Ashida H. (2012). α-N-acetylgalactosaminidase from infant-associated bifidobacteria belonging to novel glycoside hydrolase family 129 is implicated in alternative mucin degradation pathway. J Biol Chem. 2012;287(1):693-700. DOI:10.1074/jbc.M111.277384 | PubMed ID:22090027 [Kiyohara2012a]