5A87

Crystal structure of the metallo-beta-lactamase VIM-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Comparison of Verona Integron-Borne Metallo-beta-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles.

Makena, A.Duzgun, A.O.Brem, J.McDonough, M.A.Rydzik, A.M.Abboud, M.I.Saral, A.Cicek, A.C.Sandalli, C.Schofield, C.J.

(2015) Antimicrob Agents Chemother 60: 1377-1384

  • DOI: 10.1128/AAC.01768-15
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Metallo-β-lactamases (MBLs) are of increasing clinical significance; the development of clinically useful MBL inhibitors is challenged by the rapid evolution of variant MBLs. The Verona integron-borne metallo-β-lactamase (VIM) enzymes are among the m ...

    Metallo-β-lactamases (MBLs) are of increasing clinical significance; the development of clinically useful MBL inhibitors is challenged by the rapid evolution of variant MBLs. The Verona integron-borne metallo-β-lactamase (VIM) enzymes are among the most widely distributed MBLs, with >40 VIM variants having been reported. We report on the crystallographic analysis of VIM-5 and comparison of biochemical and biophysical properties of VIM-1, VIM-2, VIM-4, VIM-5, and VIM-38. Recombinant VIM variants were produced and purified, and their secondary structure and thermal stabilities were investigated by circular dichroism analyses. Steady-state kinetic analyses with a representative panel of β-lactam substrates were carried out to compare the catalytic efficiencies of the VIM variants. Furthermore, a set of metalloenzyme inhibitors were screened to compare their effects on the different VIM variants. The results reveal only small variations in the kinetic parameters of the VIM variants but substantial differences in their thermal stabilities and inhibition profiles. Overall, these results support the proposal that protein stability may be a factor in MBL evolution and highlight the importance of screening MBL variants during inhibitor development programs.


    Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom cemal.sandalli@erdogan.edu.tr christopher.schofield@chem.ox.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METALLO-BETA-LACTAMASE VIM-5A, B248Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaVIM-5
EC: 3.5.2.6
Find proteins for Q8GKX2 (Klebsiella pneumoniae)
Explore Q8GKX2 
Go to UniProtKB:  Q8GKX2
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.27α = 90
b = 78.96β = 104.82
c = 64.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references