5CZK

Structure of E. coli beta-glucuronidase bound with a novel, potent inhibitor 1-((6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(4-hydroxyphenyl)thiourea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and Inhibition of Microbiome beta-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity.

Wallace, B.D.Roberts, A.B.Pollet, R.M.Ingle, J.D.Biernat, K.A.Pellock, S.J.Venkatesh, M.K.Guthrie, L.O'Neal, S.K.Robinson, S.J.Dollinger, M.Figueroa, E.McShane, S.R.Cohen, R.D.Jin, J.Frye, S.V.Zamboni, W.C.Pepe-Ranney, C.Mani, S.Kelly, L.Redinbo, M.R.

(2015) Chem Biol 22: 1238-1249

  • DOI: 10.1016/j.chembiol.2015.08.005
  • Primary Citation of Related Structures:  
    4JKM, 4JKK, 4JKL, 5CZK

  • PubMed Abstract: 
  • The selective inhibition of bacterial β-glucuronidases was recently shown to alleviate drug-induced gastrointestinal toxicity in mice, including the damage caused by the widely used anticancer drug irinotecan. Here, we report crystal structures of re ...

    The selective inhibition of bacterial β-glucuronidases was recently shown to alleviate drug-induced gastrointestinal toxicity in mice, including the damage caused by the widely used anticancer drug irinotecan. Here, we report crystal structures of representative β-glucuronidases from the Firmicutes Streptococcus agalactiae and Clostridium perfringens and the Proteobacterium Escherichia coli, and the characterization of a β-glucuronidase from the Bacteroidetes Bacteroides fragilis. While largely similar in structure, these enzymes exhibit marked differences in catalytic properties and propensities for inhibition, indicating that the microbiome maintains functional diversity in orthologous enzymes. Small changes in the structure of designed inhibitors can induce significant conformational changes in the β-glucuronidase active site. Finally, we establish that β-glucuronidase inhibition does not alter the serum pharmacokinetics of irinotecan or its metabolites in mice. Together, the data presented advance our in vitro and in vivo understanding of the microbial β-glucuronidases, a promising new set of targets for controlling drug-induced gastrointestinal toxicity.


    Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599-3290, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-3290, USA. Electronic address: redinbo@unc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-glucuronidaseAB605Escherichia coli K-12Mutation(s): 0 
Gene Names: uidAgurAgusAb1617JW1609
EC: 3.2.1.31
Find proteins for P05804 (Escherichia coli (strain K12))
Explore P05804 
Go to UniProtKB:  P05804
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
57Z
Query on 57Z

Download CCD File 
A, B
1-[(6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl]-1-(2-hydroxyethyl)-3-(4-hydroxyphenyl)thiourea
C21 H23 N3 O3 S
GJJDKMIHKNXATK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
57ZKi:  1900   nM  BindingDB
57ZKi:  1900   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.14α = 90
b = 76.098β = 125.3
c = 125.831γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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 StatesCA98468

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence