3ISG

Structure of the class D beta-lactamase OXA-1 in complex with doripenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 11840-11847

  • DOI: 10.1021/bi901690r
  • Also Cited By: 3PAG, 3PAE

  • PubMed Abstract: 
  • The clinical efficacy of carbapenem antibiotics depends on their resistance to the hydrolytic action of beta-lactamase enzymes. The structure of the class D beta-lactamase OXA-1 as an acyl complex with the carbapenem doripenem was determined to 1.4 A ...

    The clinical efficacy of carbapenem antibiotics depends on their resistance to the hydrolytic action of beta-lactamase enzymes. The structure of the class D beta-lactamase OXA-1 as an acyl complex with the carbapenem doripenem was determined to 1.4 A resolution. Unlike most class A and class C carbapenem complexes, the acyl carbonyl oxygen in the OXA-1-doripenem complex is bound in the oxyanion hole. Interestingly, no water molecules were observed in the vicinity of the acyl linkage, providing an explanation for why carbapenems inhibit OXA-1. The side chain amine of K70 remains fully carboxylated in the acyl structure, and the resulting carbamate group forms a hydrogen bond to the alcohol of the 6alpha-hydroxyethyl moiety of doripenem. The carboxylate attached to the beta-lactam ring of doripenem is stabilized by a salt bridge to K212 and a hydrogen bond with T213, in lieu of the interaction with an arginine side chain found in most other beta-lactamase-beta-lactam complexes (e.g., R244 in the class A member TEM-1). This novel set of interactions with the carboxylate results in a major shift of the carbapenem's pyrroline ring compared to the structure of the same ring in meropenem bound to OXA-13. Additionally, bond angles of the pyrroline ring suggest that after acylation, doripenem adopts the Delta(1) tautomer. These findings provide important insights into the role that carbapenems may have in the inactivation process of class D beta-lactamases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase OXA-1
A, B
251Escherichia coliMutation(s): 0 
Gene Names: bla (oxa1)
EC: 3.5.2.6
Find proteins for P13661 (Escherichia coli)
Go to UniProtKB:  P13661
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DRW
Query on DRW

Download SDF File 
Download CCD File 
A, B
(2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid
Doripenem(open form, pyrroline tautomer form 2, SP3 connection to Thio as S isomer)
C15 H26 N4 O6 S2
RBKUPZPTQNSPAV-CFINEGTKSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.041α = 90.00
b = 71.613β = 99.18
c = 93.139γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-25 
  • Released Date: 2009-12-01 
  • Deposition Author(s): Powers, R.A.

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description