1E3U

MAD structure of OXA10 class D beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/s0969-2126(00)00534-7
  • Primary Citation of 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.


  • Organizational Affiliation

    Groupe de Cristallographie Biologique IPBS-CNRS, Toulouse, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE OXA-10
A, B, C
246Pseudomonas aeruginosaMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE OXA-10246Pseudomonas aeruginosaMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AUC
Query on AUC

Download Ideal Coordinates CCD File 
AA [auth C]
E [auth A]
GA [auth D]
HA [auth D]
IA [auth D]
AA [auth C],
E [auth A],
GA [auth D],
HA [auth D],
IA [auth D],
N [auth B],
Y [auth C],
Z [auth C]
GOLD (I) CYANIDE ION
C2 Au N2
DGOHFTDNMSZWDQ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
F [auth A]
G [auth A]
H [auth A]
BA [auth C],
CA [auth C],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
LA [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
FA [auth C]
L [auth A]
M [auth A]
DA [auth C],
EA [auth C],
FA [auth C],
L [auth A],
M [auth A],
MA [auth D],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.53α = 90
b = 82.94β = 95.03
c = 101.42γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SOLVEphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2024-10-16
    Changes: Data collection, Database references, Structure summary