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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 | + | ''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with [[Glycoside Hydrolase Family 101]] endo-α-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>. NagBb more rapidly act on GalNAcα1-''p''NP than Galβ1-3GalNAcα1-''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-α-''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-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 == | == Kinetics and Mechanism == | ||
| − | NagBb is a retaining enzyme. The stereochemistry of hydrolysis has been monitored by normal-phase HPLC using | + | 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 [[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 == | == Catalytic Residues == | ||
| − | Asp-435 in NagBb is predicted as catalytic nucleophile by the remote homology-based fold recognition method using | + | 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 [{{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> | ||
| − | # | + | #Kiyohara2012a pmid=22090027 |
| − | |||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH129]] | [[Category:Glycoside Hydrolase Families|GH129]] | ||
Revision as of 07:01, 7 March 2012
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Hisashi Ashida^^^
- Responsible Curator: ^^^Shinya Fushinobu^^^
| 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
- 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 |