5xb7

Publication Abstract from PubMed

Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have beta-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for alpha-L-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (BlArap42B) from a probiotic Bifidobacterium species cannot hydrolyze beta-galactosides. However, BlArap42B effectively hydrolyzed paeonolide and ginsenoside Rb2, plant glycosides containing an aromatic aglycone conjugated to alpha-L-arabinopyranosyl-(1,6)-beta-D-glucopyranoside. Paeonolide, a natural glycoside from the roots of the plant genus Paeonia, is not hydrolyzed by classical GH42 beta-galactosidases. X-ray crystallography revealed a unique Trp345-X12-Trp358 sequence motif at the BlArap42B active site, as compared to a Phe-X12-His motif in classical GH42 beta-galactosidases. This analysis also indicated that the C6 position of galactose is blocked by the aromatic side chains, hence allowing accommodation only of Arap lacking this carbon. Automated docking of paeonolide revealed that it can fit into the BlArap42B active site. The Glcp moiety of paeonolide stacks onto the aromatic ring of the Trp252 at subsite +1 and C4-OH is hydrogen bonded with Asp249. Moreover, the aglycone stacks against Phe421 from the neighboring monomer in the BlArap42B trimer, forming a proposed subsite +2. These results further support the notion that evolution of metabolic specialization can be tracked at the structural level in key enzymes facilitating degradation of specific glycans in an ecological niche.

Discovery of alpha-L-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.,Viborg AH, Katayama T, Arakawa T, Abou Hachem M, Lo Leggio L, Kitaoka M, Svensson B, Fushinobu S J Biol Chem. 2017 Oct 23. pii: M117.792598. doi: 10.1074/jbc.M117.792598. PMID:29061847^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.