3K4D

Crystal structure of E. coli beta-glucuronidase with the glucaro-d-lactam inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.393 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alleviating cancer drug toxicity by inhibiting a bacterial enzyme.

Wallace, B.D.Wang, H.Lane, K.T.Scott, J.E.Orans, J.Koo, J.S.Venkatesh, M.Jobin, C.Yeh, L.A.Mani, S.Redinbo, M.R.

(2010) Science 330: 831-835

  • DOI: 10.1126/science.1191175
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The dose-limiting side effect of the common colon cancer chemotherapeutic CPT-11 is severe diarrhea caused by symbiotic bacterial β-glucuronidases that reactivate the drug in the gut. We sought to target these enzymes without killing the commensal ba ...

    The dose-limiting side effect of the common colon cancer chemotherapeutic CPT-11 is severe diarrhea caused by symbiotic bacterial β-glucuronidases that reactivate the drug in the gut. We sought to target these enzymes without killing the commensal bacteria essential for human health. Potent bacterial β-glucuronidase inhibitors were identified by high-throughput screening and shown to have no effect on the orthologous mammalian enzyme. Crystal structures established that selectivity was based on a loop unique to bacterial β-glucuronidases. Inhibitors were highly effective against the enzyme target in living aerobic and anaerobic bacteria, but did not kill the bacteria or harm mammalian cells. Finally, oral administration of an inhibitor protected mice from CPT-11-induced toxicity. Thus, drugs may be designed to inhibit undesirable enzyme activities in essential microbial symbiotes to enhance chemotherapeutic efficacy.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucuronidase
A, B
605Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: uidA (gurA, gusA)
EC: 3.2.1.31
Find proteins for P05804 (Escherichia coli (strain K12))
Go to UniProtKB:  P05804
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EVA
Query on EVA

Download SDF File 
Download CCD File 
A, B
(2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid
C6 H9 N O6
YEWOHTVJCCDCCS-NTAGLIMJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EVAIC50: 586 nM BINDINGMOAD
EVAKi: 7750 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.393 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 167.653α = 90.00
b = 76.971β = 124.98
c = 125.468γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description