5Z9S

Functional and Structural Characterization of a beta-Glucosidase Involved in Saponin Metabolism from Intestinal Bacteria

Summary for 5Z9S

• Entry DOI: 10.2210/pdb5z9s/pdb
• Descriptor: Glycosyl hydrolase family 3 protein, beta-D-glucopyranose (3 entities in total)
• Functional Keywords: saponins, glucosidase, biotransformation, bifidobacterium longum, hydrolase
• Biological source: Bifidobacterium longum
• Total number of polymer chains: 2
• Total formula weight: 172323.64

Authors

Yan, S.,Wei, P.C.,Li, J.R. (deposition date: 2018-02-05, release date: 2018-03-14, Last modification date: 2023-11-22)

Primary citation

Yan, S.,Wei, P.C.,Chen, Q.,Chen, X.,Wang, S.C.,Li, J.R.,Gao, C.
Functional and structural characterization of a beta-glucosidase involved in saponin metabolism from intestinal bacteria.
Biochem. Biophys. Res. Commun., 496:1349-1356, 2018

PubMed Abstract: Saponins are natural glycosides widely used in medicine and the food industry. Although saponin metabolism in human is dependent on intestinal microbes, few involving bacteria enzymes have been identified. We cloned BlBG3, a GH3 β-glucosidase from Bifidobacterium longum, from human stool. We found that BlBG3 catalyzes the hydrolysis of glycoside furostanol and ginsenoside Rb1 at higher efficiency than other microbial β-glucosidases. Structural analysis of BlBG3 in complex with d-glucose revealed its three unique loops, which form a deep pocket and participate in substrate binding. To understand how substrate is bound to the pocket, molecular docking was performed and the binding interactions of protobioside with BlBG3 were revealed. Mutational study suggested that R484 and H642 are critical for enzymatic activity. Our study presents the first structural and functional analysis of a saponin-processing enzyme from human microbiota.

PubMed: 29421652
DOI: 10.1016/j.bbrc.2018.02.018

Experimental method

X-RAY DIFFRACTION (2.3 Å)