3PAE

Crystal structure of the K84D mutant of OXA-24/40 in complex with doripenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the Class D Carbapenemase OXA-24 from Acinetobacter baumannii in Complex with Doripenem.

Schneider, K.D.Ortega, C.J.Renck, N.A.Bonomo, R.A.Powers, R.A.Leonard, D.A.

(2011) J.Mol.Biol. 406: 583-594

  • DOI: 10.1016/j.jmb.2010.12.042
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The emergence of class D β-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfor ...

    The emergence of class D β-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D β-lactamases with carbapenemase activity are resistant to β-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6α hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.


    Related Citations: 
    • The 1.4 A crystal structure of the class D beta-lactamase OXA-1 complexed with doripenem
      Schneider, K.D.,Karpen, M.E.,Bonomo, R.A.,Leonard, D.A.,Powers, R.A.
      (2009) Biochemistry 48: 11840


    Organizational Affiliation

    Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
245Acinetobacter baumanniiMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
4J6
Query on 4J6

Download SDF File 
Download CCD File 
A, B
(4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid
Doripenem(open form, pyrroline tautomer form 1, SP2 connection to Thio)
C15 H26 N4 O6 S2
QJKQOMNNBOTMCR-PQTSNVLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 102.334α = 90.00
b = 102.334β = 90.00
c = 85.450γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-11-25
    Type: Non-polymer description
  • Version 1.3: 2016-10-05
    Type: Non-polymer description