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Difference between revisions of "Glycoside Hydrolase Family 129"
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| − | * [[Author]]: | + | * [[Author]]: [[User:Hisashi Ashida|Hisashi Ashida]] and [[User:Mayo Sato|Mayo Sato]] |
| − | * [[Responsible Curator]]: | + | * [[Responsible Curator]]: [[User:Shinya Fushinobu|Shinya Fushinobu]] |
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== Substrate specificities == | == Substrate specificities == | ||
| − | This family of glycoside hydrolases was established based on the α-''N''-acetylgalactosaminidase (NagBb) from | + | 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>. |
| − | ''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. | + | 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 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. | 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 to [[GH101]] as well as [[GH13]] α-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 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 == | ||
| − | + | Asp435 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>. 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 == | == Three-dimensional structures == | ||
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== 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: Predicted to be Asp435 in NagBb based on homology modelling <cite>Kiyohara2012a</cite>. |
| − | ;First general acid/base residue identification: '' | + | ;First [[general acid/base]] residue identification: ''Not known.'' |
| − | ;First 3-D structure: '' | + | ;First 3-D structure: ''None.'' |
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | #Kiyohara2012a pmid=22090027 | + | #Kiyohara2012a pmid=22090027 |
| + | #Naumoff2010 pmid=20556855 | ||
| + | #Naumoff2011 pmid=22295578 | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH129]] | [[Category:Glycoside Hydrolase Families|GH129]] | ||
Latest revision as of 13:15, 18 December 2021
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.
| 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 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]. Before the establishment of this family, it has been predicted as a hypothetical glycoside hydrolase-like (GHL) family GHL1 [2, 3]. 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
Asp435 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]. 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
Currently not determined experimentally.
Family Firsts
- First stereochemistry determination
- NagBb from Bifidobacterium bifidum JCM 1254 by normal-phase HPLC [1].
- First catalytic nucleophile identification
- Predicted to be Asp435 in NagBb based on homology modelling [1].
- First general acid/base residue identification
- Not known.
- First 3-D structure
- None.
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 |
- Naumoff DG (2010). GH101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. J Bioinform Comput Biol. 2010;8(3):437-51. DOI:10.1142/s0219720010004628 |
- Naumov DG (2011). [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. Mol Biol (Mosk). 2011;45(6):1073-83. | Google Books | Open Library