New to the CAZy classification? Read this first.
Want to learn more about CAZypedia? Read the CAZypedia 10th anniversary article in Glycobiology.

Difference between revisions of "Glycoside Hydrolase Family 128"

From CAZypedia
Jump to: navigation, search
Line 15: Line 15:
 
|-
 
|-
 
|'''Mechanism'''
 
|'''Mechanism'''
|retaining
+
|predicted retaining
 
|-
 
|-
 
|'''Active site residues'''
 
|'''Active site residues'''
|known/not known
+
|predicted
 
|-
 
|-
 
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
Line 29: Line 29:
  
 
== Substrate specificities ==
 
== Substrate specificities ==
Family GH128 contains &beta;-1,3-glucanases that cleave &beta;-1,3 linkages in various &beta;-glucans such as lentinan from ''Lentinula edodes'', laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'' and curdlan from ''Alcaligenes faecalis''. The first GH128 enzyme, GLU1, was cloned from ''L. edodes'' fruiting bodies (shiitake mushroom). GLU1 did not degrade &beta;-1,3-linkages within &beta;-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into (EC [{{EClink}}3.2.1.39 3.2.1.39]<cite>Sakamoto2011</cite>.
+
Family GH128 contains &beta;-1,3-glucanases that cleave &beta;-1,3 linkages in various &beta;-glucans such as lentinan from ''Lentinula edodes'', laminarin from ''Laminaria digitata'', pachyman from ''Poria cocos'', and curdlan from ''Alcaligenes faecalis''. The first GH128 enzyme, GLU1, was cloned from ''L. edodes'' fruiting bodies (shiitake mushroom). GLU1 did not degrade &beta;-1,3-linkages within &beta;-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>.
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
A GH128 enzyme, GLU1, catalyzed depolymerization of glucans composed of &beta;-1,3-linked main chains, and reaction product analysis indicated that the enzyme had an endolytic mode. The optimal pH and temperature of the enzyme for laminarin were pH 4 and at 50 °C, respectively. From the result of the three-dimensional structure prediction, GLU1 would be categorized to GH-A clan in CAZy server. Therefore, it have been inferred that GH 128 enzymes are retaining enzymes   <cite>Sakamoto2011</cite>.   
+
''L. edodes'' GLU1 catalyzed the hydrolysis of glucans composed of &beta;-1,3-linked main chains, and reaction product analysis indicated that the enzyme had an endo-hydrolytic mode of action. The optimal pH and temperature of the enzyme for laminarin were pH 4 and at 50 °C, respectively. Detailed mechanistic studies on GH128 have not been performed, but three-dimensional structure prediction has indicated that GLU1 is a member of [[Clan]] GH-A. As such, GH128 members are predicted to be [[retaining]] enzymes <cite>Sakamoto2011</cite>.   
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
From the sequence alignment of GH128 members, two conserved glutamic acids, E103 and E195 in GLU1, were expected to perform as the catalytic residues  
+
From the sequence alignment of GH128 members, two conserved glutamic acids, E103 and E195 in ''L. edodes'' GLU1, were predicted to be the residues <cite>Sakamoto2011</cite>.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The deduced sequence of GLU1 was used to predict three-dimensional structure using the Phyre server (http://www.sbg.bio.ic.ac.uk/~phyre/; 9). The result indicated that the three-dimensional structure of GLU1 matches some (b/a)8 TIM barrel structures, such as GH39 b-xylosidase (Q9ZFM2) and GH5 b-mannanase (Q4W8M3). Therefore, GH128 would be categorized to GH-A clan  <cite>Sakamoto2011</cite>.
+
A three-dimensional structure homology model of ''L. edodes'' GLU1 indicated similarity with severl (beta/alpha)<sub>8</sub>-barrel (TIM-barrel) structures, including a [[GH39]] beta-xylosidase and a [[GH5]] beta-mannanase <cite>Sakamoto2011</cite>. Therefore, GH128 has been included in [[Clan]] [http://www.cazy.org/Glycoside-Hydrolases.html GH-A].
  
 
== Family Firsts ==
 
== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
+
;First stereochemistry determination: Predicted to be [[retaining]] by membership in [[Clan]] GH-A (not experimentally verified) <cite>Sakamoto2011</cite>.
;First catalytic nucleophile identification: Content is to be added here.
+
;First catalytic nucleophile identification: Predicted by sequence alignment (not experimentally verified) <cite>Sakamoto2011</cite>.
;First general acid/base residue identification: Content is to be added here.
+
;First general acid/base residue identification: Predicted by sequence alignment (not experimentally verified) <cite>Sakamoto2011</cite>.
;First 3-D structure: Content is to be added here.
+
;First 3-D structure: Predicted by modelling to be homologous to [[Clan]] GH-A (not experimentally verified) <cite>Sakamoto2011</cite>.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
 
#Sakamoto2011 pmid=21965406
 
#Sakamoto2011 pmid=21965406
 +
 
</biblio>
 
</biblio>
  

Revision as of 09:16, 28 January 2020

Under construction icon-blue-48px.png
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

Glycoside Hydrolase Family GH128
Clan GH-A
Mechanism predicted retaining
Active site residues predicted
CAZy DB link
http://www.cazy.org/GH128.html


Substrate specificities

Family GH128 contains β-1,3-glucanases that cleave β-1,3 linkages in various β-glucans such as lentinan from Lentinula edodes, laminarin from Laminaria digitata, pachyman from Poria cocos, and curdlan from Alcaligenes faecalis. The first GH128 enzyme, GLU1, was cloned from L. edodes fruiting bodies (shiitake mushroom). GLU1 did not degrade β-1,3-linkages within β-1,3-1,4-glucans such as barley glucan, indicating the enzyme is categorized into EC 3.2.1.39 [1].

Kinetics and Mechanism

L. edodes GLU1 catalyzed the hydrolysis of glucans composed of β-1,3-linked main chains, and reaction product analysis indicated that the enzyme had an endo-hydrolytic mode of action. The optimal pH and temperature of the enzyme for laminarin were pH 4 and at 50 °C, respectively. Detailed mechanistic studies on GH128 have not been performed, but three-dimensional structure prediction has indicated that GLU1 is a member of Clan GH-A. As such, GH128 members are predicted to be retaining enzymes [1].

Catalytic Residues

From the sequence alignment of GH128 members, two conserved glutamic acids, E103 and E195 in L. edodes GLU1, were predicted to be the residues [1].

Three-dimensional structures

A three-dimensional structure homology model of L. edodes GLU1 indicated similarity with severl (beta/alpha)8-barrel (TIM-barrel) structures, including a GH39 beta-xylosidase and a GH5 beta-mannanase [1]. Therefore, GH128 has been included in Clan GH-A.

Family Firsts

First stereochemistry determination
Predicted to be retaining by membership in Clan GH-A (not experimentally verified) [1].
First catalytic nucleophile identification
Predicted by sequence alignment (not experimentally verified) [1].
First general acid/base residue identification
Predicted by sequence alignment (not experimentally verified) [1].
First 3-D structure
Predicted by modelling to be homologous to Clan GH-A (not experimentally verified) [1].

References

  1. Sakamoto Y, Nakade K, and Konno N. (2011) Endo-β-1,3-glucanase GLU1, from the fruiting body of Lentinula edodes, belongs to a new glycoside hydrolase family. Appl Environ Microbiol. 77, 8350-4. DOI:10.1128/AEM.05581-11 | PubMed ID:21965406 | HubMed [Sakamoto2011]