Crystal structure of glycoside hydrolase family 31 α-xylosidase from a soil metagenome

MeXyl31, a member of glycoside hydrolase family 31 (GH31), is the alpha-xylosidase isolated from a soil metagenomic library. The enzyme degrades alpha-xylosyl substrate such as isoprimeverose, alpha-d-xylopyranosyl-(1 -> 6)-glucopyranose. The crystal structure of MeXyl31 was determined at 1.80 angstrom resolution. MeXyl31 forms the tetrameric state. The complexed structure with a xylose in the -1 subsite (alpha-xylose binding site) shows that the enzyme strictly recognizes alpha-xylose. Structural comparison between MeXyl31 and its homologue, Aspergillus niger alpha-xylosidase in GH31, gave insights into the positive subsite of MeXyl31. First, in the tetrameric enzyme, two monomers (a catalytic monomer and the adjacent monomer), are involved in substrate recognition. Second, the adjacent monomer composes a part of positive subsites in MeXyl31. Docking simulation and site-directed mutagenesis suggested that the Arg100 from the adjacent monomer is partially involved in the recognizing of a glucopyranose of isoprimeverose.