9T06 | pdb_00009t06

Crystal structure of OXA-244 beta-lactamase K73A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.219 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Improved hydrolysis of piperacillin by OXA-48-like R214G variants, a selective advantage under piperacillin-tazobactam exposure.

Nermont, R.Oueslati, S.Aumont-Nicaise, M.Retailleau, P.Iorga, B.I.Naas, T.

(2026) Antimicrob Agents Chemother : e0126725-e0126725

  • DOI: https://doi.org/10.1128/aac.01267-25
  • Primary Citation Related Structures: 
    9T06

  • PubMed Abstract: 

    OXA-48-like carbapenemases have rapidly disseminated worldwide, becoming the most common carbapenemase in many countries, with more than 60 variants reported. Among them, OXA-244 (OXA-48-R214G) and OXA-484 (OXA-181-R214G) are increasingly reported, despite overall reduced hydrolytic activities for β-lactams, including temocillin and carbapenems. R214, located in the β5-β6 loop, through the interaction with D159, is crucial for carbapenem hydrolysis by structuring the active site. R214G variants of OXA-48-likes were analyzed by β-lactam susceptibility testing, steady-state kinetic analyses in the presence or absence of sodium hydrogen carbonate (NaHCO 3 ), molecular modeling, X-ray crystallography, and protein stability assessments using differential scanning fluorimetry (DSF). The R214G substitution in OXA-48 and OXA-181 results in reduced minimal inhibitory concentrations (MICs) for all β-lactams, except for piperacillin and piperacillin/tazobactam combination, for which MICs are increased. OXA-244 and OXA-484 displayed a better affinity for piperacillin with lower K m than for parental enzymes and thus resulted in a higher catalytic efficiency for piperacillin hydrolysis. These results were supported by docking observations, highlighting enhanced affinity when glycine is located at position 214. Overall, DSF indicated that the R214G substitution, while destabilizing the active site, enhances the global stability of the protein, especially for OXA-244. The addition of NaHCO 3 raised the activity and thermal stability of all enzymes, especially of OXA-48, which appeared more sensitive to the presence of NaHCO 3 . Although OXA-48-like R214G is considered a loss-of-function variant, our findings indicate it exhibits increased hydrolytic activity toward piperacillin, which may result in an advantage under piperacillin-tazobactam exposure and thus could contribute to the selection of these globally expanding variants.


  • Organizational Affiliation
    • Faculty of Medicine, Team 'Resist', UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB),' INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Le Kremlin-Bicêtre, France.

Macromolecule Content 

  • Total Structure Weight: 60.83 kDa 
  • Atom Count: 4,594 
  • Modeled Residue Count: 494 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
254Klebsiella pneumoniaeMutation(s): 2 
Gene Names: blaOXA-244
EC: 3.5.2.6
UniProt
Find proteins for L7UXE1 (Klebsiella pneumoniae)
Explore L7UXE1 
Go to UniProtKB:  L7UXE1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7UXE1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.219 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.456α = 90
b = 90.456β = 90
c = 163.435γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-20-PAMR-0010

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Database references