1MBL

A catalytically-impaired class A beta-lactamase: 2 Angstroms crystal structure and kinetics of the Bacillus licheniformis E166A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A catalytically-impaired class A beta-lactamase: 2 A crystal structure and kinetics of the Bacillus licheniformis E166A mutant.

Knox, J.R.Moews, P.C.Escobar, W.A.Fink, A.L.

(1993) Protein Eng. 6: 11-18


  • PubMed Abstract: 
  • In the beta-lactamase (penicillinase) of Bacillus licheniformis 749/C, site specific mutation of Glu166 to Ala caused a million-fold reduction of catalytic activity towards both penicillin and cephalosporin substrates and resulted in the stoichiometr ...

    In the beta-lactamase (penicillinase) of Bacillus licheniformis 749/C, site specific mutation of Glu166 to Ala caused a million-fold reduction of catalytic activity towards both penicillin and cephalosporin substrates and resulted in the stoichiometric accumulation of the acyl enzyme. The rate of deacylation generally slowed by as much as 10(-7) compared to the wild type. The acyl enzyme intermediate was observed by HPLC, but not by X-ray diffraction. The mutant was crystallized from methoxyPEG 5000 at pH 6.2 in space group P2(1) with Z = 4. Molecular replacement based on the wild type structure followed by refinement produced an R factor of 17.2% for 25,800 3 sigma data from 10 to 2 A. Deviations from bond and angle ideals are 0.005 A and 1.5 degrees respectively. The mutant differs very little from the wild type structure, with only 0.25 A (r.m.s.) differences in backbone atoms; the CD spectra and thermal stabilities of the two enzymes are identical. Changes in the positions of the reactive Ser70 and conserved Lys73 are not significant, suggesting that the proposed salt linkage to Glu166 in the wild type enzyme is weak or non-existent. The calculated solvent exposure of Ser70 and Lys73 increases slightly and a buried water molecule is now positioned near Lys73. The hydrolytic water seen in the native active site shifts markedly by 1.6 A, but is held in the active site by Asn170, which possibly becomes an ineffective substitute for Glu166 in activating the water for deacylation.


    Related Citations: 
    • Beta-Lactamase of Bacillus Licheniformis 749C: Refinement at 2 Angstroms Resolution and Analysis of Hydration
      Knox, J.R.,Moews, P.C.
      (1991) J.Mol.Biol. 220: 435
    • Crystallography of Penicillin-Binding Enzymes
      Knox, J.R.
      (1993) RECENT ADVANCES IN THE CHEMISTRY OF ANTI-INFECTIVE AGENTS (SPEC.PUBL.R.SOC.CHEM.,NO. 119) --: 36


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-3125.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE
A, B
256Bacillus licheniformisMutation(s): 1 
Gene Names: penP (blaP)
EC: 3.5.2.6
Find proteins for P00808 (Bacillus licheniformis)
Go to UniProtKB:  P00808
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.200α = 90.00
b = 94.100β = 104.50
c = 43.800γ = 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: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-30
    Type: Structure summary
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other