4JKL

Crystal Structure of Streptococcus agalactiae beta-glucuronidase in space group P21212


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.288 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucuronidase
A, B
602Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)Mutation(s): 0 
Find proteins for Q8E0N2 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Go to UniProtKB:  Q8E0N2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.288 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.001α = 90.00
b = 198.759β = 90.00
c = 75.573γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2015-10-21
    Type: Database references