Bacteroides dorei Beta-glucuronidase

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases.

Biernat, K.A.Pellock, S.J.Bhatt, A.P.Bivins, M.M.Walton, W.G.Tran, B.N.T.Wei, L.Snider, M.C.Cesmat, A.P.Tripathy, A.Erie, D.A.Redinbo, M.R.

(2019) Sci Rep 9: 825-825

  • DOI: https://doi.org/10.1038/s41598-018-36069-w
  • Primary Citation of Related Structures:  
    6EC6, 6ECA, 6ED1, 6ED2

  • PubMed Abstract: 

    Bacterial β-glucuronidase (GUS) enzymes cause drug toxicity by reversing Phase II glucuronidation in the gastrointestinal tract. While many human gut microbial GUS enzymes have been examined with model glucuronide substrates like p-nitrophenol-β-D-glucuronide (pNPG), the GUS orthologs that are most efficient at processing drug-glucuronides remain unclear. Here we present the crystal structures of GUS enzymes from human gut commensals Lactobacillus rhamnosus, Ruminococcus gnavus, and Faecalibacterium prausnitzii that possess an active site loop (Loop 1; L1) analogous to that found in E. coli GUS, which processes drug substrates. We also resolve the structure of the No Loop GUS from Bacteroides dorei. We then compare the pNPG and diclofenac glucuronide processing abilities of a panel of twelve structurally diverse GUS proteins, and find that the new L1 GUS enzymes presented here process small glucuronide substrates inefficiently compared to previously characterized L1 GUS enzymes like E. coli GUS. We further demonstrate that our GUS inhibitors, which are effective against some L1 enzymes, are not potent towards all. Our findings pinpoint active site structural features necessary for the processing of drug-glucuronide substrates and the inhibition of such processing.

  • Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyl hydrolase family 2, sugar binding domain protein
A, B, C, D
879Phocaeicola doreiMutation(s): 0 
Gene Names: BSEG_01974
Find proteins for C3R9X4 (Phocaeicola dorei 5_1_36/D4)
Explore C3R9X4 
Go to UniProtKB:  C3R9X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3R9X4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.663α = 90
b = 101.355β = 94.97
c = 168.6γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA098468
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA207416

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description