5Z9S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Yan, S.Wei, P.C.Chen, Q.Chen, X.Wang, S.C.Li, J.R.Gao, C.

(2018) Biochem. Biophys. Res. Commun. 496: 1349-1356

  • DOI: 10.1016/j.bbrc.2018.02.018

  • 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 Bi ...

    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.


    Organizational Affiliation

    State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycosyl hydrolase family 3 protein
A, B
796Bifidobacterium longum subsp. longum KACC 91563Mutation(s): 0 
Gene Names: bglX2
Find proteins for F8ATF7 (Bifidobacterium longum subsp. longum KACC 91563)
Go to UniProtKB:  F8ATF7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.954α = 90.00
b = 134.419β = 98.82
c = 90.285γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31470388
National Natural Science Foundation of ChinaChina31470738

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references, Source and taxonomy, Structure summary