CAZypedia - User contributions [en-ca]

User:Hisashi Ashida

2012-03-08T09:39:56Z

Hisashi Ashida:

[[Image:ashida.jpg|200px|right]]
Hisashi Ashida is a professor in the Department of Science and Technology on Food Safety, Faculty of Biology-Oriented Science and Technology, Kinki University. He graduated from Kyoto University in 1988, and received his Ph.D. degree of Agricultural Science from the same university in 2000 under the supervision of Prof. Kenji Yamamoto. He became a post-doctoral fellow at the Department of Biochemistry, Tulane University School of Medicine (Prof. Yu-Teh Li) from 2000 to 2001, and then at the Research Institute for Microbial Diseases, Osaka University (Prof. Taroh Kinoshita) from 2001 to 2004. He obtained the position of an assistant professor at Prof. Kinoshita’s laboratory in 2004. In 2006, he moved to the Graduate School of Biostudies, Kyoto University (Prof. Yamamoto), and promoted to an associate professor in 2008. He moved to Kinki University in 2012. His research interests are the metabolism of complex carbohydrates in animals and microbes. He discovered [[GH129]] <cite>Kiyohara2012a</cite>, and also contributed to the discoveries of [[GH98]] <cite>Anderson2005</cite> and [[GT76]] <cite>Kang2005</cite>.

----
<biblio>
#Kiyohara2012a 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:'' [http://dx.doi.org/10.1074/jbc.M111.277384 DOI:10.1074/jbc.M111.277384] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22090027 PMID: 22090027]
#Anderson2005 pmid=15618227
#Kang2005 pmid=15623507

</biblio>

Glycoside Hydrolase Family 129

2012-03-08T09:39:30Z

Hisashi Ashida:

{{UnderConstruction}}
* [[Author]]: ^^^Hisashi Ashida^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH129'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|Asp
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH129.html
|}
</div>


== 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 <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 ==
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 ==
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 ==

== 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 ==
<biblio>
#Kiyohara2012a 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:'' [http://dx.doi.org/10.1074/jbc.M111.277384 DOI:10.1074/jbc.M111.277384] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22090027 PMID: 22090027]
</biblio>

[[Category:Glycoside Hydrolase Families|GH129]]

User:Hisashi Ashida

2012-03-08T08:22:39Z

Hisashi Ashida: Created page with "right Hisashi Ashida is a professor in the Department of Science and Technology on Food Safety, Faculty of Biology-Oriented Science and Technology, Kin..."

[[Image:ashida.jpg|200px|right]]
Hisashi Ashida is a professor in the Department of Science and Technology on Food Safety, Faculty of Biology-Oriented Science and Technology, Kinki University. He graduated from Kyoto University in 1988, and received his Ph.D. degree of Agricultural Science from the same university in 2000 under the supervision of Prof. Kenji Yamamoto. He became a post-doctoral fellow at the Department of Biochemistry, Tulane University School of Medicine (Prof. Yu-Teh Li) from 2000 to 2001, and then at the Research Institute for Microbial Diseases, Osaka University (Prof. Taroh Kinoshita) from 2001 to 2004. He obtained the position of an assistant professor at Prof. Kinoshita’s laboratory in 2004. In 2006, he moved to the Graduate School of Biostudies, Kyoto University (Prof. Yamamoto), and promoted to an associate professor in 2008. He moved to Kinki University in 2012. His research interests are the metabolism of complex carbohydrates in animals and microbes. He discovered GH129 [1], and also contributed to the discoveries of GH98 [2] and GT76 [3].

----
<biblio>
#Kiyohara2012a Kiyohara M, Nakatomi T, Kurihara S, Fushinobu S, Suzuki H, Tanaka T, Shoda S, Kitaoka M, Katayama T, Yamamoto K, Ashida H. ''&alpha:-''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:'' [http://dx.doi.org/10.1074/jbc.M111.277384 DOI:10.1074/jbc.M111.277384] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22090027 PMID: 22090027]
#Anderson2005 pmid=15618227
#Kang2005 pmid=15623507

</biblio>

File:Ashida.jpg

2012-03-08T07:59:48Z

Hisashi Ashida:

Glycoside Hydrolase Family 129

2012-02-17T07:18:29Z

Hisashi Ashida:

{{UnderConstruction}}
* [[Author]]: ^^^Hisashi Ashida^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH129'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|Asp
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH129.html
|}
</div>


== Substrate specificities ==
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.
== 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.

== 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.

== 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 ==
<biblio>
#Cantarel2009 pmid=18838391
#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>

[[Category:Glycoside Hydrolase Families|GH129]]

Glycoside Hydrolase Family 129

2012-02-17T06:56:30Z

Hisashi Ashida:

{{UnderConstruction}}
* [[Author]]: ^^^Hisashi Ashida^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH129'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|Asp
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH129.html
|}
</div>


== Substrate specificities ==
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.
== 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.

== 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.

== 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 ==
<biblio>
#Cantarel2009 pmid=18838391
#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>

[[Category:Glycoside Hydrolase Families|GH129]]