4JKK

Crystal Structure of Streptococcus agalactiae beta-glucuronidase in space group I222


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.150 

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: https://doi.org/10.1016/j.chembiol.2015.08.005
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucuronidase602Streptococcus agalactiae 2603V/RMutation(s): 0 
Gene Names: SAG0698
EC: 3.2.1.31
UniProt
Find proteins for Q8E0N2 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Explore Q8E0N2 
Go to UniProtKB:  Q8E0N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8E0N2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.150 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.814α = 90
b = 83.829β = 90
c = 199.332γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations