5CZK | pdb_00005czk

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 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.chembiol.2015.08.005
  • Primary Citation Related Structures: 
    4JKK, 4JKL, 4JKM, 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 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.

Macromolecule Content 

  • Total Structure Weight: 139.51 kDa 
  • Atom Count: 10,059 
  • Modeled Residue Count: 1,201 
  • Deposited Residue Count: 1,210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-glucuronidase
A, B
605Escherichia coli K-12Mutation(s): 0 
Gene Names: uidAgurAgusAb1617JW1609
EC: 3.2.1.31
UniProt
Find proteins for P05804 (Escherichia coli (strain K12))
Explore P05804 
Go to UniProtKB:  P05804
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05804
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
57Z

Query on 57Z



Download:Ideal Coordinates CCD File
C [auth A],
D [auth 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
57Z BindingDB:  5CZK Ki: 1900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.256 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA98468

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary