CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 123

2016-08-17T06:40:16Z

Tomomi Sumida:

{{CuratorApproved}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|probably retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

[[Glycoside hydrolase]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]), which degrade glycosphingolipids. These enzymes hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkages. β-''N''-Acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]) are distinguished from β-hexosaminidases (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidases (EC [{{EClink}}3.2.1.52 3.2.1.52]) because β-''N''-acetylgalactosaminidases are specific to β-GalNAc linkage while β-''N''-acetylglucosaminidases are specific to β-GlcNAc linkage; β-hexosaminidases hydrolyze both β-GlcNAc and β-GalNAc linkages at a non-reducing terminus. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the founding member of this family <cite>SumidaJBC2011</cite>.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a highly specific β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to families [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] are [[retaining]] enzymes that cleave sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through a mechanism in which the 2-acetamido group of the substrate assists catalysis ([[neighboring group participation]]). GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], is a potent competitive inhibitor of NgaP <cite>SumidaJBC2011</cite>. The stereochemical outcome of substrate hydrolysis catalyzed by GH123 enzymes has not been determined. However, NgaP was proposed to be a retaining enzyme and to use substrate-assisted catalysis <cite>SumidaJBC2011</cite>, based on its inhibition by GalNAc-thiazoline. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 and Asp607 of NgaP functions as a [[general acid/base]] and a stabilizer of the 2-acetamide group of the β-GalNAc at the transition state, respectively. Point mutation analysis confirmed that Glu608 and Asp607 are integral for the activity of NgaP.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 and Asp607 of NagP function as [[general acid/base]] and a transition state stabilizer of the 2-acetamido group <cite>SumidaJBC2011</cite>.

== Three-dimensional structures ==
CpNga123 from ''Clostridium perfringens'' <cite>Noach2016</cite>.

In 2016, the crystal structures of GH123 from ''Clostridium perfringens'' (CpNga123) are determined <cite>Noach2016</cite>. CpNga123 was proved to have the activity of β-''N''-acetylgalactosaminidase. CpNga123 hydrolyzed β-GalNAc at the non-reducing end terminus but not hydrolyzed β-GlcNAc. This indicates that CpNga123 is not a β-''N''-acetylhexosaminidase but a β-''N''-acetylgalactosaminidase (EC 3.2.1.53). The crystal structures of CpNga123 (apo form and complex forms with β-GalNAc, GalNAc-F2, GA2 trisaccharide and Gb4 disaccharide) were determined. CpNga123 has a catalytic (β/α)<sub>8</sub>-barrel domain and an N-terminal β-sandwich domain. It was also revealed that a structural change of the active site was essential for forming interactions to the substrate and the substrate-assisted catalytic mechanism. Furthermore, the difference of the hydrolysis activity of the enzyme toward GA2 and Gb4 glycosphingolipids was explained by the structural difference of the complex structures.
== Family Firsts ==
;First stereochemistry determination: None reported.
;First catalytic nucleophile identification: Unknown. It has been proposed that the carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a nucleophile <cite>SumidaJBC2011</cite>.
;First general acid/base residue identification: Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP <cite>SumidaJBC2011</cite>.
;First 3-D structure: CpaNga123 from ''Clostridium perfringens'' <cite>Noach2016</cite>.

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160
#Noach2016 pmid=27038508

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

User:Tomomi Sumida

2016-08-11T10:39:09Z

Tomomi Sumida:

[[Image:Tomomi Sumida.jpg|200px|right]]

Tomomi Sumida obtained her Ph.D. from [http://www.agr.kyushu-u.ac.jp/english/ the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University], under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

* [[GH3]] β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.
* [[GH20]] β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009 SumidaOBC2012</cite>.
* [[GH123]] β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, [http://www.cazy.org/GH123.html GH123] was created as a new family of β-''N''-acetylgalactosaminidases in 2011.

----

<biblio>
#SumidaAEM2002 pmid=12406710
#SumidaJB2002 pmid=12153721
#SumidaJMB2009 pmid=19524595
#SumidaOBC2012 pmid=22367352
#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]

File:Tomomi Sumida.jpg

2016-08-11T10:35:57Z

Tomomi Sumida:

Glycoside Hydrolase Family 123

2015-03-18T01:20:57Z

Tomomi Sumida:

{{CuratorApproved}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|probably retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]) that degrade glycosphingolipids. These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminus. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycoside hydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 and Asp607 of NgaP functions as a proton donor and a stabilizer of the 2-acetamide group of the β-GalNAc at the active site. Point mutation analysis confirmed that Glu608 and Asp607 are integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 and Asp607 functions as a proton donor and a stabilizer of the 2-acetamide group of the substrate in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 123

2015-03-18T01:18:19Z

Tomomi Sumida:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|probably retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]) that degrade glycosphingolipids. These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminus. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycoside hydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 and Asp607 of NgaP functions as a proton donor and a stabilizer of the 2-acetamide group of the β-GalNAc at the active site. Point mutation analysis confirmed that Glu608 and Asp607 are integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 and Asp607 functions as a proton donor and a stabilizer of the 2-acetamide group of the substrate in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 123

2014-11-07T07:50:21Z

Tomomi Sumida:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known/not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]). These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]). Because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminal. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycohydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 of NgaP functions as a proton donor. Point mutation analysis confirmed that Glu608 is integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 functions as a proton donor in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 123

2014-11-07T07:48:41Z

Tomomi Sumida:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known/not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]). These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]). Because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminal. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycohydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 of NgaP functions as a proton donor. Point mutation analysis confirmed that Glu608 is integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 functions as a proton donor in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 123

2014-11-07T05:41:38Z

Tomomi Sumida:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known/not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]). These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]). Because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminal. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycohydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 of NgaP functions as a proton donor. Point mutation analysis confirmed that Glu608 is integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 functions as a proton donor in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 123

2014-11-07T05:40:37Z

Tomomi Sumida:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known/not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]).

These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]). Because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminal. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycohydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.

The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 of NgaP functions as a proton donor. Point mutation analysis confirmed that Glu608 is integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 functions as a proton donor in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

User:Tomomi Sumida

2014-09-29T06:54:31Z

Tomomi Sumida:

[[Image:Blank_user-200px.png|200px|right]]

Tomomi Sumida obtained her Ph.D. from [http://www.agr.kyushu-u.ac.jp/english/ the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University], under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

・[[GH3]] β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.

・[[GH20]] β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009</cite><cite>SumidaOBC2012</cite>.

・[[GH123]] β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, class [http://www.cazy.org/GH123.html GH123] was created as a new family of β-''N''-acetylgalactosaminidase in 2011.

----

<biblio>

#SumidaAEM2002 pmid=12406710

#SumidaJB2002 pmid=12153721

#SumidaJMB2009 pmid=19524595

#SumidaOBC2012 pmid=22367352

#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]

User:Tomomi Sumida

2014-09-29T04:49:53Z

Tomomi Sumida:

[[Image:Blank_user-200px.png|200px|right]]

Tomomi Sumida obtained her Ph.D. from the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University, under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

・[[GH3]] β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.

・[[GH20]] β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009</cite><cite>SumidaOBC2012</cite>.

・[[GH123]] β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, class [http://www.cazy.org/GH123.html GH123] was created as a new family of β-''N''-acetylgalactosaminidase in 2011.

----

<biblio>

#SumidaAEM2002 pmid=12406710

#SumidaJB2002 pmid=12153721

#SumidaJMB2009 pmid=19524595

#SumidaOBC2012 pmid=22367352

#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]

User:Tomomi Sumida

2014-09-29T03:07:36Z

Tomomi Sumida:

[[Image:Blank_user-200px.png|200px|right]]

Tomomi Sumida obtained her Ph.D. from the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University, under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

・[[GH3]] β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.

・[[GH20]] β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009</cite><cite>SumidaOBC2012</cite>.

・[[GH123]] β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, class [http://www.cazy.org/GH123.html GH123] was created as a new family of β-''N''-acetylgalactosaminidase in 2011.

----

<biblio>

#SumidaAEM2002 pmid=12406710

</biblio>

<biblio>

#SumidaJB2002 pmid=12153721

</biblio>

<biblio>

#SumidaJMB2009 pmid=19524595

</biblio>

<biblio>

#SumidaOBC2012 pmid=22367352

</biblio>

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]

User:Tomomi Sumida

2014-09-29T03:04:18Z

Tomomi Sumida:

[[Image:Blank_user-200px.png|200px|right]]

Tomomi Sumida obtained her Ph.D. from the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University, under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

・[http://www.cazy.org/GH3.html GH3] β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.

・[http://www.cazy.org/GH20.html GH20] β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009</cite><cite>SumidaOBC2012</cite>.

・[http://www.cazy.org/GH123.html GH123] β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, class [http://www.cazy.org/GH123.html GH123] was created as a new family of β-''N''-acetylgalactosaminidase in 2011.

----

<biblio>

#SumidaAEM2002 pmid=12406710

</biblio>

<biblio>

#SumidaJB2002 pmid=12153721

</biblio>

<biblio>

#SumidaJMB2009 pmid=19524595

</biblio>

<biblio>

#SumidaOBC2012 pmid=22367352

</biblio>

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]

User:Tomomi Sumida

2014-09-29T02:36:04Z

Tomomi Sumida:

[[Image:Blank_user-200px.png|200px|right]]

Tomomi Sumida obtained her Ph.D. from the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University, under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

・GH3 β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.

・GH20 β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009</cite><cite>SumidaOBC2012</cite>.

・GH123 β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, class GH123 was created as a new family of β-''N''-acetylgalactosaminidase in 2011.

----

<biblio>

#SumidaAEM2002 pmid=12406710

</biblio>

<biblio>

#SumidaJB2002 pmid=12153721

</biblio>

<biblio>

#SumidaJMB2009 pmid=19524595

</biblio>

<biblio>

#SumidaOBC2012 pmid=22367352

</biblio>

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]

User:Tomomi Sumida

2014-09-29T02:35:13Z

Tomomi Sumida:

[[Image:Blank_user-200px.png|200px|right]]
0 0 1 198 1131 RIKEN 9 2 1327 14.0

Tomomi Sumida obtained her Ph.D. from the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyusyu University, under the supervision of Professor Makoto Ito in 2010. She isolated the ganglioside–degrading bacterium ''Paenibacillus'' sp. strain TS12 from land soil in her doctoral research <cite>SumidaAEM2002</cite>. Strain TS12 produces a series of glycosphingolipid-degrading enzymes, such as sialidase, β-galactosidase, β-hexosaminidase, β-''N''-acetylgalactosaminidase, and β-glucocerebrosidase. She has reported the molecular cloning, characterization, and structural analysis of these novel glycosphingolipid-degrading enzymes, as follows:

・GH3 β-glucocerebrosidase (Glc4) from ''Paenibacillus'' sp. TS12 <cite>SumidaJB2002</cite>.

・GH20 β-hexosaminidase (Hex1) from ''Paenibacillus'' sp. TS12 <cite>SumidaJMB2009</cite><cite>SumidaOBC2012</cite>.

・GH123 β-''N''-acetylgalactosaminidase (NgaP) from ''Paenibacillus'' sp. TS12 <cite>SumidaJBC2011</cite>.

NgaP, which specifically hydrolyzes the non-reducing terminal β-GalNAc linkage but not β-GlcNAc linkage, is the first β-''N''-acetylgalactosaminidase (EC 3.2.1.53) to have its primary structure elucidated. Since the primary structure of NgaP is totally new, class GH123 was created as a new family of β-''N''-acetylgalactosaminidase in 2011.

----

0 0 1 35 204 RIKEN 1 1 238 14.0

<biblio>

#SumidaAEM2002 pmid=12406710

</biblio>

<biblio>

#SumidaJB2002 pmid=12153721

</biblio>

<biblio>

#SumidaJMB2009 pmid=19524595

</biblio>

<biblio>

#SumidaOBC2012 pmid=22367352

</biblio>

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>


[[Category:Contributors|Sumida,Tomomi]]