1BLH

STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF THE TETRAHEDRAL TRANSITION STATE(SLASH)INTERMEDIATE OF BETA-LACTAM HYDROLYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis.

Chen, C.C.Rahil, J.Pratt, R.F.Herzberg, O.

(1993) J.Mol.Biol. 234: 165-178

  • DOI: 10.1006/jmbi.1993.1571

  • PubMed Abstract: 
  • The crystal structure of beta-lactamase from Staphylococcus aureus inactivated by p-nitrophenyl[[N-(benzyloxycarbonyl)amino]methyl]phosphonate, a methylphosphonate monoester monoanion inhibitor, has been determined and refined at 2.3 A resolution. Th ...

    The crystal structure of beta-lactamase from Staphylococcus aureus inactivated by p-nitrophenyl[[N-(benzyloxycarbonyl)amino]methyl]phosphonate, a methylphosphonate monoester monoanion inhibitor, has been determined and refined at 2.3 A resolution. The structure reveals a tetrahedral phosphorus covalently bonded to the O gamma atom of the active site serine, Ser70. One of the oxygen atoms bonded to phosphorus is located in the oxyanion hole formed by the two main-chain nitrogen atoms of Ser70 and Gln237, and the second bonded oxygen is solvated. The (benzyloxycarbonyl)aminomethyl group is oriented towards the active site gully such that the peptide group forms compensating electrostatic interactions with polar groups on the enzyme. The benzyl group forms a hydrophobic interaction with Ile239 and an aromatic-aromatic edge-to-face interaction with Tyr105, which has undergone a conformational transition relative to the native structure. The mode of binding supports the proposal that on reaction with the enzyme, the phosphonate generates a structure analogous to the tetrahedral transition state/intermediate associated with the acylation step of a normal substrate. The disposition of the phosphonyl group in this complex is the same as that of the corresponding phosphoryl group in the complex resulting from the inhibition of trypsin by diisopropylphosphofluoridate. The structure is consistent with a mechanism of inactivation that follows an associative pathway, proceeding via a transition state/intermediate in which phosphorus is penta-co-ordinated, forming a trigonal bipyramidal geometry with the phosphonyl donor (p-nitrophenol) and acceptor (Ser70 O gamma atom) in apical positions. A model of this transition state can be accommodated in the active site of beta-lactamase without any steric hindrance. A model of the tetrahedral transition state associated with the acylation step by benzyl penicillin has been derived. Because of the conformational rigidity of the fused rings of penicillin molecules, the orientation of the substrate is fixed once the tetrahedral carbonyl carbon and its ligands are superimposed on the phosphonate group. The outcome is that the carboxylate substituent on the thiazolidine ring forms a salt bridge with Lys234, and the preferred puckering of the ring is that observed in the crystal structure of ampicillin, the so-called "open" conformer.


    Related Citations: 
    • 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) Biochem.J. 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
    • Penicillin-Binding and Degrading Enzymes
      Herzberg, O.,Moult, J.
      (1991) Curr.Opin.Struct.Biol. 1: 946
    • 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
    • Inhibition of Beta-Lactamase by Clavulanate. Trapped Intermediates in Cryocrystallographic Studies
      Chen, C.C.H.,Herzberg, O.
      (1992) J.Mol.Biol. 224: 1103
    • 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: 9504


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FOS
Query on FOS

Download SDF File 
Download CCD File 
A
[[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE
C9 H12 N O5 P
WUNKRZNFNIYEPN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.960α = 90.00
b = 94.200β = 90.00
c = 138.930γ = 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: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance