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Difference between revisions of "Glycoside Hydrolase Family 129"
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* [[Author]]: ^^^Hisashi Ashida^^^ | * [[Author]]: ^^^Hisashi Ashida^^^ | ||
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== Substrate specificities == | == Substrate specificities == | ||
| − | This family of glycoside hydrolases was | + | This family of glycoside hydrolases was established based on the 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 acts more rapidly 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]). This specificity 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]]. As such, NagBb may be appropriately referred to as a 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 <cite>Kiyohara2012a</cite>. GH129 is distantly related | + | 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 to [[GH101]] as well as [[GH13]] α-amylases; members of these latter two families are also classified as retaining enzymes. |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | Asp-435 in NagBb is predicted as catalytic nucleophile by | + | Asp-435 in NagBb is predicted as catalytic nucleophile by remote homology-based fold recognition 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 the so-called "fixer": the third invariant catalytic residue conserved in [[GH101]] and [[GH13]] enzymes. The general acid/base residue is in GH129 unknown. |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | Currently not determined experimentally. | |
== Family Firsts == | == Family Firsts == | ||
;First stereochemistry determination: NagBb from ''Bifidobacterium bifidum'' JCM 1254 by normal-phase HPLC <cite>Kiyohara2012a</cite>. | ;First stereochemistry determination: NagBb from ''Bifidobacterium bifidum'' JCM 1254 by normal-phase HPLC <cite>Kiyohara2012a</cite>. | ||
| − | ;First catalytic nucleophile identification: | + | ;First catalytic nucleophile identification: ''To be determined experimentally.'' |
| − | ;First general acid/base residue identification: | + | ;First general acid/base residue identification: ''To be determined experimentally.'' |
| − | ;First 3-D structure: | + | ;First 3-D structure: ''To be determined experimentally.'' |
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | #Kiyohara2012a | + | #Kiyohara2012a pmid=22090027] |
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH129]] | [[Category:Glycoside Hydrolase Families|GH129]] | ||
Revision as of 10:40, 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 | |
| http://www.cazy.org/GH129.html | |
Substrate specificities
This family of glycoside hydrolases was established based on the α-N-acetylgalactosaminidase (NagBb) from Bifidobacterium bifidum JCM 1254, which shows slight sequence similarity with GH101 endo-α-N-acetylgalactosaminidases [1]. NagBb acts more rapidly on GalNAcα1-pNP than Galβ1-3GalNAcα1-pNP, therefore its substrate specificity is quite different from GH101 enzymes (EC 3.2.1.97). This specificity is also different from those of previously known exo-α-N-acetylgalactosaminidases (EC 3.2.1.49) in GH27, GH36 and GH109. As such, NagBb may be appropriately referred to as a 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 to GH101 as well as GH13 α-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 α-amylase 1 (TVAI) from Thermoactinomyces vulgaris R-47 (PDB code 1JI1) as a template [1]. 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.
Three-dimensional structures
Currently not determined experimentally.
Family Firsts
- First stereochemistry determination
- NagBb from Bifidobacterium bifidum JCM 1254 by normal-phase HPLC [1].
- First catalytic nucleophile identification
- To be determined experimentally.
- First general acid/base residue identification
- To be determined experimentally.
- First 3-D structure
- To be determined experimentally.
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 |