1KGG

STRUCTURE OF BETA-LACTAMASE GLU166GLN:ASN170ASP MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Relocation of the catalytic carboxylate group in class A beta-lactamase: the structure and function of the mutant enzyme Glu166-->Gln:Asn170-->Asp.

Chen, C.C.Herzberg, O.

(1999) Protein Eng. 12: 573-579


  • PubMed Abstract: 
  • The hydrolysis of beta-lactam antibiotics by the serine-beta-lactamases proceeds via an acyl-enzyme intermediate. In the class A enzymes, a key catalytic residue, Glu166, activates a water molecule for nucleophilic attack on the acyl-enzyme intermedi ...

    The hydrolysis of beta-lactam antibiotics by the serine-beta-lactamases proceeds via an acyl-enzyme intermediate. In the class A enzymes, a key catalytic residue, Glu166, activates a water molecule for nucleophilic attack on the acyl-enzyme intermediate. The active site architecture raises the possibility that the location of the catalytic carboxylate group may be shifted while still maintaining close proximity to the hydrolytic water molecule. A double mutant of the Staphylococcus aureus PC1 beta-lactamase, E166Q:N170D, was produced, with the carboxylate group shifted to position 170 of the polypeptide chain. A mutant protein, E166Q, without a carboxylate group and with abolished deacylation, was produced as a control. The kinetics of the two mutant proteins have been analyzed and the crystal structure of the double mutant protein has been determined. The kinetic data confirmed that deacylation was restored in E166Q:N170D beta-lactamase, albeit not to the level of the wild-type enzyme. In addition, the kinetics of the double mutant enzyme follows progressive inactivation, characterized by initial fast rates and final slower rates. The addition of ammonium sulfate increases the size of the initial burst, consistent with stabilization of the active form of the enzyme by salt. The crystal structure reveals that the overall fold of the E166Q:N170D enzyme is similar to that of native beta-lactamase. However, high crystallographic temperature factors are associated with the ohm-loop region and some of the side chains, including Asp170, are partially or completely disordered. The structure provides a rationale for the progressive inactivation of the Asp170-containing mutant, suggesting that the flexible ohm-loop may be readily perturbed by the substrate such that Asp170's carboxylate group is not always poised to facilitate hydrolysis.


    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
    • 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, 9600 Gudelsky Drive, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BETA-LACTAMASE)
A
258Staphylococcus 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.178 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.000α = 90.00
b = 94.800β = 90.00
c = 138.600γ = 90.00
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-28
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-04
    Type: Advisory, Refinement description