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Difference between revisions of "Glycoside Hydrolase Family 137"

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(fixed missing biblio tag)
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== Substrate specificities ==
 
== Substrate specificities ==
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>.
+
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.
 
 
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
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== Catalytic Residues ==
 
== Catalytic Residues ==
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen<cite>Ndeh2017</cite>.  
+
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>.  
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII<cite>Ndeh2017</cite>.
+
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.
  
 
== Family Firsts ==
 
== Family Firsts ==
 
;First stereochemistry determination: Not Known.
 
;First stereochemistry determination: Not Known.
 
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.
 
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.
;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.
+
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.
+
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.
  
 
== References ==
 
== References ==

Latest revision as of 11:24, 27 January 2020

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Glycoside Hydrolase Family GH137
Clan GH-x
Mechanism Unknown
Active site residues known
CAZy DB link
http://www.cazy.org/GH137.html


Substrate specificities

The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) [1].

Kinetics and Mechanism

Unknown

Catalytic Residues

The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen [1].

Three-dimensional structures

The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII [1].

Family Firsts

First stereochemistry determination
Not Known.
First catalytic nucleophile/base identification
Inferred to be Glu159 in BT0996 [1].
First general acid/base residue identification
Inferred to be Glu240 in BT0996 [1].
First 3-D structure
The first structure determination for GH137 was of BT0996 from the organism Bacteroides thetaiotaomicon [1].

References

  1. Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, and Gilbert HJ. (2017) Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature. 544, 65-70. DOI:10.1038/nature21725 | PubMed ID:28329766 | HubMed [Ndeh2017]
  2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 37, D233-8. DOI:10.1093/nar/gkn663 | PubMed ID:18838391 | HubMed [Cantarel2009]
  3. 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. Download PDF version.
    [DaviesSinnott2008]
All Medline abstracts: PubMed | HubMed