5XB7

GH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis subsp. lactis Bl-04

Summary for 5XB7

• Entry DOI: 10.2210/pdb5xb7/pdb
• Descriptor: Beta-galactosidase, SULFATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: alpha-l-arabinopyranosidase, gh42, arabinopyranoside, hydrolase
• Biological source: Bifidobacterium animalis subsp. lactis
• Total number of polymer chains: 6
• Total formula weight: 484235.36

Authors

Viborg, A.H.,Katayama, T.,Arakawa, T.,Abou Hachem, M.,Lo Leggio, L.,Kitaoka, M.,Svensson, B.,Fushinobu, S. (deposition date: 2017-03-16, release date: 2017-11-01, Last modification date: 2023-11-22)

Primary citation

Viborg, A.H.,Katayama, T.,Arakawa, T.,Abou Hachem, M.,Lo Leggio, L.,Kitaoka, M.,Svensson, B.,Fushinobu, S.
Discovery of alpha-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.
J. Biol. Chem., 292:21092-21101, 2017

PubMed Abstract: 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 β-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for α-l-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (Arap42B) from a probiotic species cannot hydrolyze β-galactosides. However, Arap42B effectively hydrolyzed paeonolide and ginsenoside Rb2, plant glycosides containing an aromatic aglycone conjugated to α-l-arabinopyranosyl-(1,6)-β-d-glucopyranoside. Paeonolide, a natural glycoside from the roots of the plant genus is not hydrolyzed by classical GH42 β-galactosidases. X-ray crystallography revealed a unique Trp--Trp sequence motif at the Arap42B active site, as compared with a Phe--His motif in classical GH42 β-galactosidases. This analysis also indicated that the C6 position of galactose is blocked by the aromatic side chains, hence allowing accommodation only of Ara lacking this carbon. Automated docking of paeonolide revealed that it can fit into the Ara42B active site. The Glc moiety of paeonolide stacks onto the aromatic ring of the Trp at subsite +1 and C4-OH is hydrogen bonded with Asp Moreover, the aglycone stacks against Phe from the neighboring monomer in the Ara42B 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.

PubMed: 29061847
DOI: 10.1074/jbc.M117.792598

Experimental method

X-RAY DIFFRACTION (2 Å)