Difference between revisions of "Glycoside Hydrolase Family 62"

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Author: Harry Gilbert and ^^^Casper Wilkens^^^
Responsible Curator: Harry Gilbert

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 both eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases and the majority act on xylose moieties in xylan and arabinose moieties in arabinan that are single substituted with α-1,2 and α-1,3-L-arabinofuranose side chains [1] with K_cat ranging from 0.3 to 180 s^-1 on wheat arabinoxylan [2, 3, 4]. However, a single GH62 enzyme from Pencillium oxalicum exclusively act on the α-1,3-L-arabinofuranose side chains [5]. The GH62 enzymes also display limited non-specific arabinofuranosidase activity; for example the arabinofuranosidases exhibit no [6] or very little [2, 3] activity against 4-nitrophenyl α-L-arabinofuranoside. Several of these enzymes contain carbohydrate binding modules that target cellulose- [6] or xylan- [7].

Kinetics and Mechanism

GH62 enzymes are inverting enzymes as first shown by NMR [4].

Catalytic Residues

Asp (general acid) and Glu (general base), as suggested by tertiary structures [2, 3, 8] and supported by site-directed mutagenesis and kinetic data [2, 3].

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 [2, 3, 8]. The predicted catalytic general acid, catalytic general base and pKa modulator [9] were also confirmed by mutagenesis data [2, 3]. 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 substrate backbone were identified for Streptomyces coelicolor α-L-arabinofuranosidase A (ScAbf62A) in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR [2]. In this respect a conserved tyrosine, present on a mobile loop, was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site [10]. Remarkably, the xylan main chain bound in two orientations in ScAbf62A and Streptomyces thermoviolaceus α-L-arabinofuranosidase A, as may be required to position both single α-1,2- and α-1,3-Araf in subsite -1 for productive binding in the active site pocket [2, 3].

Family Firsts

First sterochemistry determination: Determined for Aspergillus nidulans α-L-arabinofuranosidase A by proton NMR [4].
First general acid residue identification: 3D structural data [2, 3, 8] in concert with supporting mutagenesis data [2, 3].
First general base residue identification: 3D structural data [2, 3, 8] in concert with supporting mutagenesis data [2, 3].
First 3-D structure: Several papers in 2014 reveal the 5-fold β-propeller fold [2, 3, 8].

References

All Medline abstracts: PubMed

@@ Line 33: / Line 33: @@
 == Three-dimensional structures ==
-Based on its location in [[clan]] F, enzymes from family GH62s are predicted to display a 5-fold &beta;-propeller fold. This hypothesis was confirmed by three papers published in 2014 <cite>Maehara2014 Siguier2014 Wang2014</cite>. The predicted catalytic general acid, catalytic general base and pKa modulator <cite>Vincent1997</cite> were also confirmed by mutagenesis data <cite>Maehara2014 Wang2014</cite>. 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 substrate backbone were identified for ''Streptomyces coelicolor'' &alpha;-L-arabinofuranosidase A in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR  <cite>Maehara2014</cite>. In this respect a conserved tyrosine, present on a mobile loop,  was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site <cite>Contesini2017</cite>.
+Based on its location in [[clan]] F, enzymes from family GH62s are predicted to display a 5-fold &beta;-propeller fold. This hypothesis was confirmed by three papers published in 2014 <cite>Maehara2014 Siguier2014 Wang2014</cite>. The predicted catalytic general acid, catalytic general base and pKa modulator <cite>Vincent1997</cite> were also confirmed by mutagenesis data <cite>Maehara2014 Wang2014</cite>. 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 substrate backbone were identified for ''Streptomyces coelicolor'' &alpha;-L-arabinofuranosidase A (ScAbf62A) in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR  <cite>Maehara2014</cite>. In this respect a conserved tyrosine, present on a mobile loop,  was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site <cite>Contesini2017</cite>. Remarkably, the xylan main chain bound in two orientations in ScAbf62A and ''Streptomyces thermoviolaceus'' &alpha;-L-arabinofuranosidase A, as may be required to position both single α-1,2- and α-1,3-Araf in subsite -1 for productive binding in the active site pocket <cite>Maehara2014 Wang2014</cite>.
 == Family Firsts ==