1K55

OXA 10 class D beta-lactamase at pH 7.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases.

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

(2001) Proc Natl Acad Sci U S A 98: 14280-14285

  • DOI: 10.1073/pnas.241442898
  • Primary Citation of Related Structures:  
    1K54, 1K55, 1K56, 1K57

  • PubMed Abstract: 

    • beta-Lactamases are the resistance enzymes for beta-lactam antibiotics, of which four classes are known. beta-lactamases hydrolyze the beta-lactam moieties of these antibiotics, rendering them inactive. It is shown herein that the class D OXA-10 beta-lactamase depends critically on an unusual carbamylated lysine as the basic residue for both the enzyme acylation and deacylation steps of catalysis ...

    beta-Lactamases are the resistance enzymes for beta-lactam antibiotics, of which four classes are known. beta-lactamases hydrolyze the beta-lactam moieties of these antibiotics, rendering them inactive. It is shown herein that the class D OXA-10 beta-lactamase depends critically on an unusual carbamylated lysine as the basic residue for both the enzyme acylation and deacylation steps of catalysis. The formation of carbamylated lysine is reversible. Evidence is presented that this enzyme is dimeric and carbamylated in living bacteria. High-resolution x-ray structures for the native enzyme were determined at pH values of 6.0, 6.5, 7.5, and 8.5. Two dimers are present per asymmetric unit. One monomer in each dimer was carbamylated at pH 6.0, whereas all four monomers were fully carbamylated at pH 8.5. At the intermediate pH values, one monomer of each dimer was carbamylated, and the other showed a mixture of carbamylated and non-carbamylated lysines. It would appear that, as the pH increased for the sample, additional lysines were "titrated" by carbamylation. A handful of carbamylated lysines are known from protein crystallographic data, all of which have been attributed roles in structural stabilization (mostly as metal ligands) of the proteins. This paper reports a previously unrecognized role for a noncoordinated carbamylate lysine as a basic residue involved in mechanistic reactions of an enzyme, which indicates another means for expansion of the catalytic capabilities of the amino acids in nature beyond the 20 common amino acids in development of biological catalysts.

    Related Citations: 
    • 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
    • The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotic
      Golemi, D., Maveyraud, L., Vakulenko, S., Tranier, S., Ishiwata, A., Kotra, L.P., Samama, J.P., Mobashery, S.
      (2000) J Am Chem Soc 122: 6132
    Organizational Affiliation: 

    Groupe de Cristallographie Biologique, Institut de Pharmacologie et de Biologie Structurale du Centre National de la Recherche Scientifique, 205 Route de Narbonne, 31077-Toulouse Cedex, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta lactamase OXA-10A, B246Pseudomonas aeruginosaMutation(s): 1 
Gene Names: bla, oxa10, pse2
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta lactamase OXA-10C, D246Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla, oxa10, pse2
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
AA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
K [auth A],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
K [auth A],
L [auth A],
M [auth A],
S [auth B],
T [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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: 1.39 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.514α = 90
b = 82.285β = 95.44
c = 101.713γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance