Functional and structural characterization of a β-glucosidase involved in saponin metabolism from intestinal bacteria

Highlights: • Bifidobacterium longum are involved in the metabolism of saponins. • BlBG3 shows higher efficiency to saponins than known bacterial β-glucosidases. • First structure of β-glucosidase from intestinal bacteria to hydrolyze saponins. • A special binding pocket differs to other structural available GH3 β-glucosidases. • Molecular docking revealed the binding interactions of substrate with BlBG3. 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.