4Y0O | pdb_00004y0o

Crystal structure of OXA-58, a carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii.

• PDB DOI: https://doi.org/10.2210/pdb4Y0O/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-02-06 Released: 2016-01-13 
• Deposition Author(s): Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D., Kumar, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.240 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D beta-Lactamase of Acinetobacter baumannii.

Pratap, S., Katiki, M., Gill, P., Kumar, P., Golemi-Kotra, D.

(2015) Antimicrob Agents Chemother 60: 75-86

• PubMed: 26459904 
• DOI: https://doi.org/10.1128/AAC.01393-15
• Primary Citation Related Structures: 
  4Y0O, 4Y0T, 4Y0U


• PubMed Abstract: 
  

  Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are a subgroup of class D β-lactamases, which are enzymes that hydrolyze β-lactams. They have attracted interest due to the emergence of multidrug-resistant Acinetobacter baumannii, which is not responsive to treatment with carbapenems, the usual antibiotics of choice for this bacterium. Unlike other class D β-lactamases, these enzymes efficiently hydrolyze carbapenem antibiotics. To explore the structural requirements for the catalysis of carbapenems by these enzymes, we determined the crystal structure of the OXA-58 CHDL of A. baumannii following acylation of its active-site serine by a 6α-hydroxymethyl penicillin derivative that is a structural mimetic for a carbapenem. In addition, several point mutation variants of the active site of OXA-58, as identified by the crystal structure analysis, were characterized kinetically. These combined studies confirm the mechanistic relevance of a hydrophobic bridge formed over the active site. This structural feature is suggested to stabilize the hydrolysis-productive acyl-enzyme species formed from the carbapenem substrates of this enzyme. Furthermore, our structural studies provide strong evidence that the hydroxyethyl group of carbapenems samples different orientations in the active sites of CHDLs, and the optimum orientation for catalysis depends on the topology of the active site allowing proper closure of the active site. We propose that CHDLs use the plasticity of the active site to drive the mechanism of carbapenem hydrolysis toward efficiency.

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Organizational Affiliation: 
• Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.
Department of Biology, York University, Toronto, Canada.
Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India [e-mail] [e-mail].
Department of Biology, York University, Toronto, Canada Department of Chemistry, York University, Toronto, Canada [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.5 kDa 
• Atom Count: 2,060 
• Modeled Residue Count: 243 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	280	Acinetobacter baumannii	Mutation(s): 0  Gene Names: blaOXA-58, bla-oxa58 EC: 3.5.2.6
UniProt
Find proteins for Q2TR58 (Acinetobacter baumannii) Explore Q2TR58  Go to UniProtKB:  Q2TR58

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.240 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.074	α = 90
b = 67.038	β = 90
c = 93.515	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D., Kumar, P.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary