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Difference between revisions of "Glycoside Hydrolase Family 129"
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<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | ||
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* [[Author]]: ^^^Hisashi Ashida^^^ | * [[Author]]: ^^^Hisashi Ashida^^^ | ||
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^ | * [[Responsible Curator]]: ^^^Shinya Fushinobu^^^ | ||
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|- | |- | ||
|'''Clan''' | |'''Clan''' | ||
| − | | | + | |none |
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
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|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |not known |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
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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 α-''N''-acetylgalactosaminidase (NagBb) from |
| − | ''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with [[GH101]] endo-α-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>. NagBb more rapidly | + | ''Bifidobacterium bifidum'' JCM 1254, which shows slight sequence similarity with [[GH101]] endo-α-''N''-acetylgalactosaminidases <cite>Kiyohara2012a</cite>. NagBb more rapidly acts on GalNAcα1-''p''NP than Galβ1-3GalNAcα1-''p''NP; therefore its substrate specificity is quite different from [[GH101]] 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 [[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. |
== 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 GalNAcα1-''p''NP as a substrate <cite>Kiyohara2012a</cite>. GH129 is distantly related with [[GH101]] as well as [[GH13]] 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 [[GH13]] 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 [[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 [[GH13]] α-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 "fixer", the third invariant catalytic residue conserved in [[GH101]] and [[GH13]] enzymes. General acid/base residue is unknown. |
== Three-dimensional structures == | == Three-dimensional structures == | ||
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== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: NagBb from ''Bifidobacterium bifidum'' JCM 1254 by normal-phase HPLC | + | ;First stereochemistry determination: NagBb from ''Bifidobacterium bifidum'' JCM 1254 by normal-phase HPLC <cite>Kiyohara2012a</cite>. |
;First catalytic nucleophile identification: | ;First catalytic nucleophile identification: | ||
;First general acid/base residue identification: | ;First general acid/base residue identification: | ||
Revision as of 02:47, 12 November 2012
This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.
- Author: ^^^Hisashi Ashida^^^
- Responsible Curator: ^^^Shinya Fushinobu^^^
| Glycoside Hydrolase Family GH129 | |
| Clan | none |
| Mechanism | retaining |
| Active site residues | not known |
| CAZy DB link | |
| https://www.cazy.org/GH129.html | |
Substrate specificities
This family of glycoside hydrolases was recently established for α-N-acetylgalactosaminidase (NagBb) from Bifidobacterium bifidum JCM 1254, which shows slight sequence similarity with GH101 endo-α-N-acetylgalactosaminidases [1]. NagBb more rapidly acts on GalNAcα1-pNP than Galβ1-3GalNAcα1-pNP; 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.
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 [1]. GH129 is distantly related with GH101 as well as GH13 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 GH13 α-amylase 1 (TVAI) from Thermoactinomyces vulgaris R-47 (PDB code 1JI1) as a template [1]. Asp-330 in NagBb may be "fixer", the third invariant catalytic residue conserved in GH101 and GH13 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 [1].
- First catalytic nucleophile identification
- First general acid/base residue identification
- First 3-D structure
References
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Kiyohara M, Nakatomi T, Kurihara S, Fushinobu S, Suzuki H, Tanaka T, Shoda S, Kitaoka M, Katayama T, Yamamoto K, Ashida H. 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 Jan 2;287(1):693-700.
Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out: DOI:10.1074/jbc.M111.277384 PMID: 22090027