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Difference between revisions of "Glycoside Hydrolase Family 128"
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|'''Mechanism''' | |'''Mechanism''' | ||
| − | |retaining | + | |predicted retaining |
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |predicted |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
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== Substrate specificities == | == 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 | + | 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 [{{EClink}}3.2.1.39 3.2.1.39] <cite>Sakamoto2011</cite>. |
== Kinetics and Mechanism == | == 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 <cite>Sakamoto2011</cite>. | |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | From the sequence alignment of GH128 members, two conserved glutamic acids, E103 and E195 in GLU1, were | + | 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 == | ||
| − | + | 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: | + | ;First stereochemistry determination: Predicted to be [[retaining]] by membership in [[Clan]] GH-A (not experimentally verified) <cite>Sakamoto2011</cite>. |
| − | ;First catalytic nucleophile identification: | + | ;First catalytic nucleophile identification: Predicted by sequence alignment (not experimentally verified) <cite>Sakamoto2011</cite>. |
| − | ;First general acid/base residue identification: | + | ;First general acid/base residue identification: Predicted by sequence alignment (not experimentally verified) <cite>Sakamoto2011</cite>. |
| − | ;First 3-D structure: | + | ;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
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.
- Author: ^^^Yuichi Sakamoto^^^
- Responsible Curator: ^^^Yuichi Sakamoto^^^
| Glycoside Hydrolase Family GH128 | |
| Clan | GH-A |
| Mechanism | predicted retaining |
| Active site residues | predicted |
| CAZy DB link | |
| https://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
- Error fetching PMID 21965406: