1KGF

STRUCTURE OF BETA-LACTAMASE ASN 170 GLN MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Elimination of the hydrolytic water molecule in a class A beta-lactamase mutant: crystal structure and kinetics.

Zawadzke, L.E.Chen, C.C.Banerjee, S.Li, Z.Wasch, S.Kapadia, G.Moult, J.Herzberg, O.

(1996) Biochemistry 35: 16475-16482

  • DOI: 10.1021/bi962242a
  • Primary Citation of Related Structures:  1KGE

  • PubMed Abstract: 
  • Two site-directed mutant enzymes of the class A beta-lactamase from Staphylococcus aureus PC1 were produced with the goal of blocking the site that in the native enzyme is occupied by the proposed hydrolytic water molecule. The crystal structures of ...

    Two site-directed mutant enzymes of the class A beta-lactamase from Staphylococcus aureus PC1 were produced with the goal of blocking the site that in the native enzyme is occupied by the proposed hydrolytic water molecule. The crystal structures of these two mutant enzymes, N170Q and N170M, have been determined and refined at 2.2 and 2.0 A, respectively. They reveal that the side chain of Gln 170 displaces the water molecule, whereas that of Met170 does not. In both cases, the catalytic rates with benzylpenicillin are reduced by 10(4) compared with the native enzyme. With nitrocefin, the N170Q mutant enzyme exhibits an approximately 800-fold reduced rate compared with the native enzyme and in addition, a fast initial burst with stoichiometry of 1 mol of degraded nitrocefin/mol of enzyme. Stopped-flow kinetic experiments establish that the rate constant of the burst is 250 s-1, a value comparable with the rate of acylation of the native enzyme. Two structurally based mechanisms that explain the kinetic properties of the N170Q beta-lactamase are proposed, both invoking a deacylation-impaired enzyme due to the elimination of the hydrolytic water molecule. The catalytic rate of the N170M mutant enzyme with nitrocefin is reduced by approximately 50-fold compared with the native enzyme, and the slow progressive inhibition that is revealed indicates that the hydrolysis proceeds via a branched pathway mechanism. This is consistent with the structural data that show that the water site is preserved and that Met170 occupies part of the space that is required for substrate binding. The short contacts between the substrate and the enzyme may lead to structure perturbation and inactivation.


    Related Citations: 
    • An Engineered Staphylococcus Aureus Pc1 Beta-Lactamase that Hydrolyses Third-Generation Cephalosporins
      Zawadzke, L.E.,Smith, T.J.,Herzberg, O.
      (1995) Protein Eng. 8: 1275
    • Structure and Kinetics of the Beta-Lactamase Mutants S70A and K73H from Staphylococcus Aureus Pc1
      Chen, C.C.,Smith, T.J.,Kapadia, G.,Wasch, S.,Zawadzke, L.E.,Coulson, A.,Herzberg, O.
      (1996) Biochemistry 35: 12251
    • Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 A Resolution
      Herzberg, O.,Moult, J.
      (1987) Science 236: 694
    • Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0
      Herzberg, O.
      (1991) J.Mol.Biol. 217: 701


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE
A
258Staphylococcus aureusGene Names: blaZ
EC: 3.5.2.6
Find proteins for P00807 (Staphylococcus aureus)
Go to UniProtKB:  P00807
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.300α = 90.00
b = 94.800β = 90.00
c = 140.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
XENGENdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance