CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.

Difference between revisions of "Glycoside Hydrolase Family 158"

From CAZypedia
Jump to navigation Jump to search
Line 34: Line 34:
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
As a family within clan GH-A, GH158 members were inferred to be retaining enzymes. Retention of anomeric stereochemistry was experimentally confirmed by <sup>1</sup>H NMR on the product of hydrolysis of 2-chloro-4-nitrophenyl laminaribioside by BuGH158 from Bacteroides uniformis [2]. As such, these enzymes follow the classical Koshland double-displacement mechanism, which proceed via a covalent glycosyl-enzyme intermediate.
+
As a family within clan GH-A, GH158 members were inferred to be retaining enzymes. Retention of anomeric stereochemistry was experimentally confirmed by <sup>1</sup>H NMR on the product of hydrolysis of 2-chloro-4-nitrophenyl laminaribioside by BuGH158 from Bacteroides uniformis <cite>Dejean2019</cite>. As such, these enzymes follow the classical Koshland double-displacement mechanism, which proceed via a covalent glycosyl-enzyme intermediate.
 
== Catalytic Residues ==
 
== Catalytic Residues ==
The catalytic nucleophile and catalytic acid/base residues of BuGH158 were determined to be E220 and E137 [2]. This glutamate pair is located on loops immediately following beta-strands 7 (nucleophile) and 4 (acid/base), consistent with all other clan GH-A enzymes.
+
The catalytic nucleophile and catalytic acid/base residues of BuGH158 were determined to be E220 and E137 <cite>Dejean2019</cite>. This glutamate pair is located on loops immediately following β-strands 7 (nucleophile) and 4 (acid/base), consistent with all other clan GH-A enzymes.
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The X-ray crystal structure of BuGH158 from Bacteroides uniformis determined by multi-wavelength anomalous dispersion represents the founding structural representative of this family [2]. The 1.8 A structure reveal in addition to an N-terminal (a/b)8 TIM barrel domain, which is a hallmark of clan GH-A structures, a C-terminal eight-stranded immunoglobulin (Ig)-like domain that makes extensive contacts with the TIM barrel. A loop from the Ig-like domain extends over the TIM barrel to shape the active site cleft.
+
The X-ray crystal structure of BuGH158 from ''Bacteroides uniformis'' determined by multi-wavelength anomalous dispersion represents the founding structural representative of this family <cite>Dejean2019</cite>. The 1.8 Å structure reveal in addition to an N-terminal (α/β)<sub>8</sub> TIM barrel domain, which is a hallmark of clan GH-A structures, a C-terminal eight-stranded immunoglobulin (Ig)-like domain that makes extensive contacts with the TIM barrel. A loop from the Ig-like domain extends over the TIM barrel to shape the active site cleft <cite>Dejean2019</cite>.
 
== Family Firsts ==
 
== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
+
;First stereochemistry determination: Retention of anomeric stereochemistry of hydrolysis product in BuGH158 from Bacteroides uniformis by NMR <cite>Dejean2019</cite>.
;First catalytic nucleophile identification: Content is to be added here.
+
;First catalytic nucleophile identification: E220 in BuGH158 from Bacteroides uniformis by structural study and kinetic analysis of site-directed mutant <cite>Dejean2019</cite>.
;First general acid/base residue identification: Content is to be added here.
+
;First general acid/base residue identification: E137 in BuGH158 from Bacteroides uniformis by structural study and kinetic analysis of site-directed mutant <cite>Dejean2019</cite>.
;First 3-D structure: Content is to be added here.
+
;First 3-D structure: BuGH158 from Bacteroides uniformis by X-ray crystallography <cite>Dejean2019</cite>.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
 
#Helbert2019 pmid=30850540
 
#Helbert2019 pmid=30850540
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+
#Dejean2019
 
</biblio>
 
</biblio>
  
 
[[Category:Glycoside Hydrolase Families|GH158]]
 
[[Category:Glycoside Hydrolase Families|GH158]]

Revision as of 10:32, 20 March 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 GH158
Clan GH-A
Mechanism retaining
Active site residues known
CAZy DB link
http://www.cazy.org/GH158.html


Substrate specificities

Members of family 158 have been shown to display activity towards β(1,3)-glucans, making it the fourth clan GH-A family known to contain β(1,3)-glucanase activity, alongside GH17, GH128, and GH148. The founding member of this family, Vvad_PD1638 from Victivallis vadensis, was shown to be active on carboxymethyl-curdlan in a high-throughput screen [1].

BuGH158 from the prominent human gut symbiont Bacteroides uniformis was the first GH158 member to receive detailed characterization [2]. BuGH158 is an endo β(1,3)-glucanase with high specificity towards laminarin from Laminaria digitata, a β(1,3)-glucan with single β(1,6)-glucose branches. BuGH158 is unable to tolerate more extensive branching as evidenced by poor activity towards other β(1,3)-glucans with longer, more frequent branches like laminarin from Eisenia bicyclis and yeast β-glucan [2]. The unbranched, linear β(1,3)-glucan curdlan was also not effectively hydrolyzed by BuGH158, due the glucans poor solubility in water (Vvad_PD1638 described above was active on a curdlan proxy that was chemically modified to increase water-solubility [1]).

Kinetics and Mechanism

As a family within clan GH-A, GH158 members were inferred to be retaining enzymes. Retention of anomeric stereochemistry was experimentally confirmed by 1H NMR on the product of hydrolysis of 2-chloro-4-nitrophenyl laminaribioside by BuGH158 from Bacteroides uniformis [2]. As such, these enzymes follow the classical Koshland double-displacement mechanism, which proceed via a covalent glycosyl-enzyme intermediate.

Catalytic Residues

The catalytic nucleophile and catalytic acid/base residues of BuGH158 were determined to be E220 and E137 [2]. This glutamate pair is located on loops immediately following β-strands 7 (nucleophile) and 4 (acid/base), consistent with all other clan GH-A enzymes.

Three-dimensional structures

The X-ray crystal structure of BuGH158 from Bacteroides uniformis determined by multi-wavelength anomalous dispersion represents the founding structural representative of this family [2]. The 1.8 Å structure reveal in addition to an N-terminal (α/β)8 TIM barrel domain, which is a hallmark of clan GH-A structures, a C-terminal eight-stranded immunoglobulin (Ig)-like domain that makes extensive contacts with the TIM barrel. A loop from the Ig-like domain extends over the TIM barrel to shape the active site cleft [2].

Family Firsts

First stereochemistry determination
Retention of anomeric stereochemistry of hydrolysis product in BuGH158 from Bacteroides uniformis by NMR [2].
First catalytic nucleophile identification
E220 in BuGH158 from Bacteroides uniformis by structural study and kinetic analysis of site-directed mutant [2].
First general acid/base residue identification
E137 in BuGH158 from Bacteroides uniformis by structural study and kinetic analysis of site-directed mutant [2].
First 3-D structure
BuGH158 from Bacteroides uniformis by X-ray crystallography [2].

References

  1. Helbert W, Poulet L, Drouillard S, Mathieu S, Loiodice M, Couturier M, Lombard V, Terrapon N, Turchetto J, Vincentelli R, and Henrissat B. (2019). Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space. Proc Natl Acad Sci U S A. 2019;116(13):6063-6068. DOI:10.1073/pnas.1815791116 | PubMed ID:30850540 [Helbert2019]
  2. [Dejean2019]