6ECA

Lactobacillus rhamnosus Beta-glucuronidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucuronidase
A, B
627Lacticaseibacillus rhamnosusMutation(s): 0 
Gene Names: BGK71_00200CCE29_06935DBP98_01505PY66_04435PY91_01090
EC: 3.2.1.31
UniProt
Find proteins for A0A2A5L2J1 (Lacticaseibacillus rhamnosus)
Explore A0A2A5L2J1 
Go to UniProtKB:  A0A2A5L2J1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2A5L2J1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.8α = 90
b = 154.8β = 90
c = 241.906γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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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