4UWO

Native di-zinc VIM-26. Leu224 in VIM-26 from Klebsiella pneumoniae has implications for drug binding.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.555 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural and Biochemical Characterization of Vim-26 Show that Leu224 Has Implications for the Substrate Specificity of Vim Metallo-Beta-Lactamases.

Leiros, H.S.Edvardsen, K.S.W.Bjerga, G.E.K.Samuelsen, O.

(2015) FEBS J. 282: 1031

  • DOI: 10.1111/febs.13200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During the last decades antimicrobial resistance has become a global health problem. Metallo-β-lactamases (MBLs) which are broad-spectrum β-lactamases that inactivate virtually all β-lactams including carbapenems, are contributing to this health prob ...

    During the last decades antimicrobial resistance has become a global health problem. Metallo-β-lactamases (MBLs) which are broad-spectrum β-lactamases that inactivate virtually all β-lactams including carbapenems, are contributing to this health problem. In this study a novel MBL variant, termed VIM-26, identified in a Klebsiella pneumoniae isolate was studied. VIM-26 belongs to the Verona integron-encoded metallo-β-lactamase (VIM) family of MBLs and is a His224Leu variant of the well-characterized VIM-1 variant. In this study, we report the kinetic parameters, minimum inhibitory concentrations and crystal structures of a recombinant VIM-26 protein, and compare them to previously published data on VIM-1, VIM-2 and VIM-7. The kinetic parameters and minimum inhibitory concentration determinations show that VIM-26, like VIM-7, has higher penicillinase activity but lower cephalosporinase activity than VIM-1 and VIM-2. The four determined VIM-26 crystal structures revealed mono- and di-zinc forms, where the Zn1 ion has distorted tetrahedral coordination geometry with an additional water molecule (W2) at a distance of 2.6-3.7 Å, which could be important during catalysis. The R2 drug binding site in VIM-26 is more open compared to VIM-2 and VIM-7 and neutrally charged due to Leu224 and Ser228. Thus, the VIM-26 drug binding properties are different from the VIM-2 (Tyr224/Arg228) and VIM-7 (His224/Arg228) structures, indicating a role of these residues in the substrate specificity.


    Organizational Affiliation

    Norwegian Structural Biology Centre, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METALLO-BETA-LACTAMASE VIM-26
B
266Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaVIM-26
Find proteins for E5BDC6 (Klebsiella pneumoniae)
Go to UniProtKB:  E5BDC6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.555 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.634α = 90.00
b = 67.882β = 92.39
c = 40.231γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references
  • Version 2.0: 2018-05-09
    Type: Atomic model, Data collection