1BLC

INHIBITION OF BETA-LACTAMASE BY CLAVULANATE: TRAPPED INTERMEDIATES IN CRYOCRYSTALLOGRAPHIC STUDIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies.

Chen, C.C.Herzberg, O.

(1992) J.Mol.Biol. 224: 1103-1113


  • PubMed Abstract: 
  • Crystallographic studies of the complex between beta-lactamase and clavulanate reveal a structure of two acyl-enzymes with covalent bonds at the active site Ser70, representing two different stages of inhibitor degradation alternately occupying the a ...

    Crystallographic studies of the complex between beta-lactamase and clavulanate reveal a structure of two acyl-enzymes with covalent bonds at the active site Ser70, representing two different stages of inhibitor degradation alternately occupying the active site. Models that are consistent with biochemical data are derived from the electron density map and refined at 2.2 A resolution: cis enamine, in which the carboxylate group of the clavulanate molecule makes a salt bridge with Lys234 of beta-lactamase; decarboxylated trans enamine, which is oriented away from Lys234. For both acyl-enzymes, the carbonyl oxygen atom of the ester group occupies the oxyanion hole in a manner similar to that found in inhibitor binding to serine proteases. Whereas the oxygen atom in the trans product is optimally positioned in the oxyanion hole, that of the cis product clashes with the main-chain nitrogen atom of Ser70 and the beta-carbon atom of the adjacent Ala69. In contrast to cis to trans isomerization in solution that relieves the steric strain inherent in a cis double bond, at the enzyme-inhibitor interface two additional factors play an important role. The salt bridge enhances the stability of the cis product, while the steric strain introduced by the short contacts with the protein reduces its stability.


    Related Citations: 
    • Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 Angstroms Resolution
      Herzberg, O.,Moult, J.
      (1987) Science 236: 694
    • Structural Basis for the Inactivation of the P54 Mutant of Beta-Lactamase from Staphylococcus Aureus Pc1
      Herzberg, O.,Kapadia, G.,Blanco, B.,Smith, T.S.,Coulson, A.
      (1991) Biochemistry 30: 9503
    • Penicillin-Binding and Degrading Enzymes
      Herzberg, O.,Moult, J.
      (1991) Curr.Opin.Struct.Biol. 1: 946
    • The Crystal Structure of Beta-Lactamase from Staphylococcus Aureus at 0.5Nm Resolution
      Moult, J.,Sawyer, L.,Herzberg, O.,Jones, C.L.,Coulson, A.F.W.,Green, D.W.,Harding, M.M.,Ambler, R.P.
      (1985) J.Biochem.(Tokyo) 225: 167
    • Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 Angstroms Resolution
      Herzberg, O.
      (1991) J.Mol.Biol. 217: 701
    • Structure of a Phosphonate-Inhibited Beta-Lactamase: An Analog of the Tetrahedral Transition State(Slash)Intermediate of Beta-Lactam Hydrolysis
      Chen, C.C.H.,Rahil, J.,Pratt, R.F.,Herzberg, O.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute, University of Maryland, Rockville 20850.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE
A
257Staphylococcus aureusGene Names: blaZ
EC: 3.5.2.6
Find proteins for P00807 (Staphylococcus aureus)
Go to UniProtKB:  P00807
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CEM
Query on CEM

Download SDF File 
Download CCD File 
A
N-(1-CARBOXY-2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-CISPROPENYL)AMINE
C8 H11 N O5
DIQBZADGQQVQIO-WHFQOLMOSA-N
 Ligand Interaction
TEM
Query on TEM

Download SDF File 
Download CCD File 
A
N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE
C7 H11 N O3
FXITUJNZFYVSNC-RCYFRSRISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.100α = 90.00
b = 88.000β = 90.00
c = 141.300γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance