3HBR

Crystal structure of OXA-48 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases.

Docquier, J.D.Calderone, V.De Luca, F.Benvenuti, M.Giuliani, F.Bellucci, L.Tafi, A.Nordmann, P.Botta, M.Rossolini, G.M.Mangani, S.

(2009) Chem Biol 16: 540-547

  • DOI: 10.1016/j.chembiol.2009.04.010
  • Primary Citation of Related Structures:  
    3HBR

  • PubMed Abstract: 
  • Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) are enzymes found in important Gram-negative pathogens (mainly Acinetobacter baumannii and Enterobacteriaceae) that confer resistance to beta-lactam antibiotics, and notably carbapenems. The crys ...

    Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) are enzymes found in important Gram-negative pathogens (mainly Acinetobacter baumannii and Enterobacteriaceae) that confer resistance to beta-lactam antibiotics, and notably carbapenems. The crystal structure of the OXA-48 carbapenemase was determined at pH 7.5 and at a resolution of 1.9 A. Surprisingly, and by contrast with OXA-24, the only other CHDL of known crystal structure, the structure of OXA-48 was similar to OXA-10, an enzyme devoid of carbapenemase activity, indicating that the hydrolysis of these compounds could depend on subtle changes in the active site region. Moreover, the active site groove of OXA-48 was different from that of OXA-24 in shape, dimensions, and charge distribution. Molecular dynamics pointed to the functional relevance of residues located in or close to the beta5-beta6 loop and allowed us to propose a mechanism for carbapenem hydrolysis by OXA-48.


    Related Citations: 
    • The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotics
      Golemi, D., Maveyraud, L., Vakulenko, S., Tranier, S., Ishiwata, A., Kotra, L.P., Samama, J.P., Mobashery, S.
      (2000) J Am Chem Soc 122: 6132
    • Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases
      Golemi, D., Maveyraud, L., Vakulenko, S., Samama, J.P., Mobashery, S.
      (2001) Proc Natl Acad Sci U S A 98: 14280

    Organizational Affiliation

    Dipartimento di Biologia Molecolare, Università di Siena, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OXA-48ABCD265Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla OXA-48bla_2bla_3blaOXA-48B6R99_29845G5626_30690KPE71T_00045SAMEA3649466_05396SAMEA3673128_05462SAMEA3729780_05587
EC: 3.5.2.6
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, B, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A,B,C,DL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.701α = 90
b = 107.185β = 111.04
c = 80.787γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance