3IF6

Crystal structure of OXA-46 beta-lactamase from P. aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the narrow-spectrum OXA-46 class D beta-lactamase: relationship between active-site lysine carbamylation and inhibition by polycarboxylates

Docquier, J.D.Benvenuti, M.Calderone, V.Giuliani, F.Kapetis, D.De Luca, F.Rossolini, G.M.Mangani, S.

(2010) Antimicrob.Agents Chemother. 54: 2167-2174

  • DOI: 10.1128/AAC.01517-09

  • PubMed Abstract: 
  • Class D beta-lactamases represent a heterogeneous group of active-site serine beta-lactamases that show an extraordinary panel of functional features and substrate profiles, thus representing relevant models for biochemical and structural studies. OX ...

    Class D beta-lactamases represent a heterogeneous group of active-site serine beta-lactamases that show an extraordinary panel of functional features and substrate profiles, thus representing relevant models for biochemical and structural studies. OXA-46 is a narrow-spectrum enzyme belonging to the OXA-2 subgroup which was found in a Pseudomonas aeruginosa clinical isolate from northern Italy. In this work, we obtained the three-dimensional structure of OXA-46, which shows the overall fold of active serine beta-lactamases and a dimeric quaternary structure. Significant differences with currently available structures of class D beta-lactamases were found in the loops located close to the active site, which differ in length and conformation. Interestingly, the three subunits present in the asymmetric unit showed some structural heterogeneity, only one of which presented a carbamylated lysine recognized as an important functional feature of class D enzymes. The carbamylation state of residue Lys75 appeared to be associated with different shapes and dimensions of the active site. Moreover, a tartrate molecule from the crystallization buffer was found in the active site of the noncarbamylated subunits, which interacts with catalytically relevant residues. The OXA-46 crystal asymmetric units thus interestingly present the structures of the free carbamylated active site and of the ligand-bound uncarbamylated active site, offering the structural basis for investigating the potential of new scaffolds of beta-lactamase inhibitors.


    Related Citations: 
    • OXA-46, a new class D beta-lactamase of narrow substrate specificity encoded by a blaVIM-1-containing integron from a Pseudomonas aeruginosa clinical isolate
      Giuliani, F.,Docquier, J.D.,Riccio, M.L.,Pagani, L.,Rossolini, G.M.
      (2005) Antimicrob.Agents Chemother. 49: 1973


    Organizational Affiliation

    Dipartimento di Biologia Molecolare, Università di Siena, Siena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OXA-46 oxacillinase
A
266Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaOXA (blaOXA-46)
EC: 3.5.2.6
Find proteins for Q8GRH0 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q8GRH0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
OXA-46 oxacillinase
B
266Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaOXA (blaOXA-46)
EC: 3.5.2.6
Find proteins for Q8GRH0 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q8GRH0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
OXA-46 oxacillinase
C
266Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaOXA (blaOXA-46)
EC: 3.5.2.6
Find proteins for Q8GRH0 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q8GRH0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
B
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, C
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.211 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 123.838α = 90.00
b = 123.838β = 90.00
c = 327.915γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-19
    Type: Database references