4X56

Structure of the class D Beta-Lactamase OXA-160 V130D in Acyl-Enzyme Complex with Ceftazidime


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D beta-Lactamases from Acinetobacter baumannii.

Mitchell, J.M.Clasman, J.R.June, C.M.Kaitany, K.C.LaFleur, J.R.Taracila, M.A.Klinger, N.V.Bonomo, R.A.Wymore, T.Szarecka, A.Powers, R.A.Leonard, D.A.

(2015) Biochemistry 54: 1976-1987

  • DOI: 10.1021/bi501547k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The carbapenem-hydrolyzing class D β-lactamases OXA-23 and OXA-24/40 have emerged worldwide as causative agents for β-lactam antibiotic resistance in Acinetobacter species. Many variants of these enzymes have appeared clinically, including OXA-160 an ...

    The carbapenem-hydrolyzing class D β-lactamases OXA-23 and OXA-24/40 have emerged worldwide as causative agents for β-lactam antibiotic resistance in Acinetobacter species. Many variants of these enzymes have appeared clinically, including OXA-160 and OXA-225, which both contain a P → S substitution at homologous positions in the OXA-24/40 and OXA-23 backgrounds, respectively. We purified OXA-160 and OXA-225 and used steady-state kinetic analysis to compare the substrate profiles of these variants to their parental enzymes, OXA-24/40 and OXA-23. OXA-160 and OXA-225 possess greatly enhanced hydrolytic activities against aztreonam, ceftazidime, cefotaxime, and ceftriaxone when compared to OXA-24/40 and OXA-23. These enhanced activities are the result of much lower Km values, suggesting that the P → S substitution enhances the binding affinity of these drugs. We have determined the structures of the acylated forms of OXA-160 (with ceftazidime and aztreonam) and OXA-225 (ceftazidime). These structures show that the R1 oxyimino side-chain of these drugs occupies a space near the β5-β6 loop and the omega loop of the enzymes. The P → S substitution found in OXA-160 and OXA-225 results in a deviation of the β5-β6 loop, relieving the steric clash with the R1 side-chain carboxypropyl group of aztreonam and ceftazidime. These results reveal worrying trends in the enhancement of substrate spectrum of class D β-lactamases but may also provide a map for β-lactam improvement.


    Organizational Affiliation

    ∥Departments of Medicine, Pharmacology, Biochemistry, and Molecular Biology and Microbiology, Case Western Reserve University and Research Service, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Class D beta-lactamase OXA-160
A
245Acinetobacter baumanniiMutation(s): 1 
Gene Names: blaOXA-160
Find proteins for D2XKK9 (Acinetobacter baumannii)
Go to UniProtKB:  D2XKK9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAZ
Query on CAZ

Download SDF File 
Download CCD File 
A
ACYLATED CEFTAZIDIME
C17 H19 N5 O7 S2
VEHPZKIFULQYFS-BZXVCXBKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.307α = 90.00
b = 102.307β = 90.00
c = 87.151γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR15AI082416-02
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR15AI094489

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-25
    Type: Database references
  • Version 1.2: 2015-04-01
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Source and taxonomy