1E4D | pdb_00001e4d

Structure of OXA10 beta-lactamase at pH 8.3

• PDB DOI: https://doi.org/10.2210/pdb1E4D/pdb

• Classification: BETA-LACTAMASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2000-07-03 Released: 2001-01-12 
• Deposition Author(s): Maveyraud, L., Golemi, D., Kotra, L.P., Tranier, S., Vakulenko, S., Mobashery, S., Samama, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.243 (Depositor) 
• R-Value Work: 
  0.198 (Depositor), 0.193 (DCC) 

Starting Model: experimental

Literature

Insights Into Class D Beta-Lactamases are Revealed by the Crystal Structure of the Oxa10 Enzyme from Pseudomonas Aeruginosa

Maveyraud, L., Golemi, D., Kotra, L.P., Tranier, S., Vakulenko, S., Mobashery, S., Samama, J.P.

(2000) Structure 8: 1289

• PubMed: 11188693 
• DOI: https://doi.org/10.1016/s0969-2126(00)00534-7
• Primary Citation Related Structures: 
  1E3U, 1E4D


• PubMed Abstract: 
  

  beta-lactam antibiotic therapies are commonly challenged by the hydrolytic activities of beta-lactamases in bacteria. These enzymes have been grouped into four classes: A, B, C, and D. Class B beta-lactamases are zinc dependent, and enzymes of classes A, C, and D are transiently acylated on a serine residue in the course of the turnover chemistry. While class A and C beta-lactamases have been extensively characterized by biochemical and structural methods, class D enzymes remain the least studied despite their increasing importance in the clinic. The crystal structure of the OXA10 class D beta-lactamase has been solved to 1.66 A resolution from a gold derivative and MAD phasing. This structure reveals that beta-lactamases from classes D and A, despite very poor sequence similarity, share a similar overall fold. An additional beta strand in OXA10 mediates the association into dimers characterized by analytical ultracentrifugation. Major differences are found when comparing the molecular details of the active site of this class D enzyme to the corresponding regions in class A and C beta-lactamases. In the native structure of the OXA10 enzyme solved to 1.8 A, Lys-70 is carbamylated. Several features were revealed by this study: the dimeric structure of the OXA10 beta-lactamase, an extension of the substrate binding site which suggests that class D enzymes may bind other substrates beside beta-lactams, and carbamylation of the active site Lys-70 residue. The CO2-dependent activity of the OXA10 enzyme and the kinetic properties of the natural OXA17 mutant protein suggest possible relationships between carbamylation, inhibition of the enzyme by anions, and biphasic behavior of the enzyme.

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Organizational Affiliation: 
• Groupe de Cristallographie Biologique IPBS-CNRS, Toulouse, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 112.18 kDa 
• Atom Count: 8,883 
• Modeled Residue Count: 979 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE OXA-10	A, B, C, D	246	Pseudomonas aeruginosa	Mutation(s): 1  EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa) Explore P14489  Go to UniProtKB:  P14489

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	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], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth A], O [auth B], P [auth B], U [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.243 (Depositor) 
• R-Value Work:  0.198 (Depositor), 0.193 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.279	α = 90
b = 82.436	β = 95.89
c = 101.165	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-12 
Deposition Author(s): Maveyraud, L., Golemi, D., Kotra, L.P., Tranier, S., Vakulenko, S., Mobashery, S., Samama, J.P.

Revision History  

• Version 1.0: 2001-01-12
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description