Glycoside Hydrolase Family 62

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Glycoside Hydrolase Family GH62
Clan	GH-F
Mechanism	inverting
Active site residues	Known
CAZy DB link
https://www.cazy.org/GH62.html

Substrate specificities

This small family of glycoside hydrolases comprises an equal number of eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases that specifically cleave either α-1,2 or α-1,3-L-arabinofuranose side chains from xylans [1, 2]. The enzymes will not act on xylose moieties in xylan that are decorated at both O2 and O3 with an arabinose side chain. The GH62 enzymes also display limited non-specific arabinofuranosidase activity; for example the arabinofuranosidases exhibit no [1] or very little [3, 4] activity against 4-nitrophenyl α-L-arabinofuranoside. Several of these enzymes contain cellulose- [1] or xylan- [5] binding CBMs.

Kinetics and Mechanism

While the catalytic mechanism of this family have not been formerly determined, likely reflecting the extremely quick rate of mutarotation displayed by arabinose, the enzyme is predicted to display a single displacement or inverting mechanism. This prediction is based on the location of GH62 in clan F, the same clan occupied by GH43, which is an inverting family. Prior to 3D structural data the catalytic residues were predicted from sequence homology with GH43 enzymes, given that both the catalytic mechanism and the catalytic apparatus are conserved in glycoside hydrolase families belonging to the same clan. Thus [6] predicts that the catalytic general acid and general base will be a Glu and Asp, respectively, while a second Asp modulates the pKa of the general acid.

Catalytic Residues

Asp (general acid) and Glu (general base), as suggested by tertiary structures [3, 4, 7] and supported by site-directed mutagenesis and kinetic data [3, 4].

Three-dimensional structures

Based on its location in clan F, enzymes from family GH62s are predicted to display a 5-fold β-propeller fold. This hypothesis was confirmed by three papers published in 2014 [3, 4, 7]. The predicted catalytic general acid, catalytic general base and pKa modulator [6] were also confirmed by mutagenesis data [3, 4]. The active site arabinose-containing pocket opens up into a cleft or channel that binds the xylooligosaccharides and thus the xylan chain. The residues that interact with the polysaccharide backbone were identified [3]. In this respect a conserved tyrosine was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site. The tyrosine is on a mobile loop and molecular dynamics suggest that its location is influenced by substrate entering the active site [8]

Contesini

.. y mobile loop

Family Firsts

First sterochemistry determination: No direct experimental proof but 3D structural information point to an inverting mechanism [3, 4, 7].
First general acid residue identification: 3D structural data [3, 4, 7] in concert with supporting mutagenesis data [3, 4].
First general base residue identification: 3D structural data [3, 4, 7] in concert with supporting mutagenesis data [3, 4].
First 3-D structure: Several papers in 2014 reveal the 5-fold β-propeller fold [3, 4, 7].

References

All Medline abstracts: PubMed