2WHG | pdb_00002whg

Crystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.254 (Depositor) 
  • R-Value Work: 
    0.200 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Biochemical and Structural Characterization of the Subclass B1 Metallo-{Beta}-Lactamase Vim-4.

Lassaux, P.Traore, D.A.K.Loisel, E.Favier, A.Docquier, J.D.Sohier, J.S.Laurent, C.Bebrone, C.Frere, J.M.Ferrer, J.L.Galleni, M.

(2011) Antimicrob Agents Chemother 55: 1248

  • DOI: https://doi.org/10.1128/AAC.01486-09
  • Primary Citation Related Structures: 
    2WHG

  • PubMed Abstract: 

    The metallo-β-lactamase VIM-4, mainly found in Pseudomonas aeruginosa or Acinetobacter baumannii, was produced in Escherichia coli and characterized by biochemical and X-ray techniques. A detailed kinetic study performed in the presence of Zn²+ at concentrations ranging from 0.4 to 100 μM showed that VIM-4 exhibits a kinetic profile similar to the profiles of VIM-2 and VIM-1. However, VIM-4 is more active than VIM-1 against benzylpenicillin, cephalothin, nitrocefin, and imipenem and is less active than VIM-2 against ampicillin and meropenem. The crystal structure of the dizinc form of VIM-4 was solved at 1.9 Å. The sole difference between VIM-4 and VIM-1 is found at residue 228, which is Ser in VIM-1 and Arg in VIM-4. This substitution has a major impact on the VIM-4 catalytic efficiency compared to that of VIM-1. In contrast, the differences between VIM-2 and VIM-4 seem to be due to a different position of the flapping loop and two substitutions in loop 2. Study of the thermal stability and the activity of the holo- and apo-VIM-4 enzymes revealed that Zn²+ ions have a pronounced stabilizing effect on the enzyme and are necessary for preserving the structure.


  • Organizational Affiliation
    • Laboratoire de Macromolecules Biologiques, Centre d'Ingénierie des Protéines, Université de Liège, Allée du 6 Août B6, Sart-Tilman, 4000 Liège, Belgium.

Macromolecule Content 

  • Total Structure Weight: 49.53 kDa 
  • Atom Count: 3,969 
  • Modeled Residue Count: 460 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VIM-4 METALLO-BETA-LACTAMASE
A, B
230Pseudomonas aeruginosaMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for Q8KRJ3 (Pseudomonas aeruginosa)
Explore Q8KRJ3 
Go to UniProtKB:  Q8KRJ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KRJ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.254 (Depositor) 
  • R-Value Work:  0.200 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.39α = 90
b = 46.22β = 105.24
c = 105.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description