3FV7

OXA-24 beta-lactamase complex with SA4-44 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase.

Bou, G.Santillana, E.Sheri, A.Beceiro, A.Sampson, J.M.Kalp, M.Bethel, C.R.Distler, A.M.Drawz, S.M.Pagadala, S.R.Van den Akker, F.Bonomo, R.A.Romero, A.Buynak, J.D.

(2010) J.Am.Chem.Soc. 132: 13320-13331

  • DOI: 10.1021/ja104092z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Ps ...

    Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2'-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC(50) values against OXA-24 and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs WT) to 338 ± 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K(i) (500 ± 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k(inact)/K(i) = 0.21 ± 0.02 μM(-1)  s(-1)). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2'-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed.


    Related Citations: 
    • Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis.
      Santillana, E.,Beceiro, A.,Bou, G.,Romero, A.
      (2007) Proc.Natl.Acad.Sci.USA 104: 5354


    Organizational Affiliation

    Instituto de Investigación Biomédica de A Coruña (INIBIC), Complejo Hospitalario Universitario A Coruña, 15006-A Coruña, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase OXA-24
A
244Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-33 (bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40)
Find proteins for Q8RLA6 (Acinetobacter baumannii)
Go to UniProtKB:  Q8RLA6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MXS
Query on MXS

Download SDF File 
Download CCD File 
A
(2S)-2-[[2-methanoyl-7-(methoxycarbonylamino)indolizin-3-yl]amino]-3-methyl-3-sulfino-butanoic acid
C16 H19 N3 O7 S
NSEWARQIMLZRTO-LBPRGKRZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MXSKi: 2300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.390α = 90.00
b = 102.390β = 90.00
c = 84.220γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
CNSrefinement
XDSdata reduction
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance