Glycoside Hydrolase Family 137

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• Author: Alan Cartmell
• Responsible Curator: Alan Cartmell

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Glycoside Hydrolase Family GH137
Clan	None
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

BT0996 was active both on intact RGII and on Chain B released from RGII [1]. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) [1]. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose.

Catalytic Residues

The catalytic residues were shown to be a pair of glutamates. The catalytic residue assignment was made based on both structural, substrate and product complexes, and mutagenic information. Glu159 and Glu240 were mutated to Ala and Gln. E159Q and E240A and E240Q were completely inactive, whilst E159A was only 26 fold less active. Despite the activity of E159A, these were the only residues that ablated activity. 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 [2]. 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 GH-A. 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. 2017;544(7648):65-70. DOI:10.1038/nature21725 |
2. Davies G and Henrissat B. (1995). Structures and mechanisms of glycosyl hydrolases. Structure. 1995;3(9):853-9. DOI:10.1016/S0969-2126(01)00220-9 |