1BMC

STRUCTURE OF A ZINC METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold.

Carfi, A.Pares, S.Duee, E.Galleni, M.Duez, C.Frere, J.M.Dideberg, O.

(1995) EMBO J. 14: 4914-4921

  • Also Cited By: 1DXK, 1X8G, 1X8H, 1X8I, 2FM6, 2FU6, 2FU7, 2FU8, 2FU9, 2GFJ, 2GFK, 2GKL, 5DPX

  • PubMed Abstract: 
  • The 3-D structure of Bacillus cereus (569/H/9) beta-lactamase (EC 3.5.2.6), which catalyses the hydrolysis of nearly all beta-lactams, has been solved at 2.5 A resolution by the multiple isomorphous replacement method, with density modification and p ...

    The 3-D structure of Bacillus cereus (569/H/9) beta-lactamase (EC 3.5.2.6), which catalyses the hydrolysis of nearly all beta-lactams, has been solved at 2.5 A resolution by the multiple isomorphous replacement method, with density modification and phase combination, from crystals of the native protein and of a specially designed mutant (T97C). The current model includes 212 of the 227 amino acid residues, the zinc ion and 10 water molecules. The protein is folded into a beta beta sandwich with helices on each external face. To our knowledge, this fold has never been observed. An approximate internal molecular symmetry is found, with a 2-fold axis passing roughly through the zinc ion and suggesting a possible gene duplication. The active site is located at one edge of the beta beta sandwich and near the N-terminal end of a helix. The zinc ion is coordinated by three histidine residues (86, 88 and 149) and a water molecule. A sequence comparison of the relevant metallo-beta-lactamases, based on this protein structure, highlights a few well-conserved amino acid residues. The structure shows that most of these residues are in the active site. Among these, aspartic acid 90 and histidine 210 participate in a proposed catalytic mechanism for beta-lactam hydrolysis.


    Related Citations: 
    • An X-Ray-Crystallographic Study of Beta-Lactamase II from Bacillus Cereus at 0.35 Nm Resolution
      Sutton, B.J.,Artymiuk, P.J.,Cordero-Borboa, A.E.,Little, C.,Phillips, D.C.,Waley, S.G.
      (1987) Biochem.J. 248: 181
    • The Amino Acid Sequence of the Zinc-Requiring Beta-Lactamase II from the Bacterium Bacillus Cereus 569
      Ambler, R.P.,Daniel, M.,Fleming, J.,Hermoso, J.M.,Pang, C.,Waley, S.G.
      (1985) FEBS Lett. 189: 207


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel (CEA-CNRS), Laboratoire de Cristallographie Macromoléculaire, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METALLO-BETA-LACTAMASE
A
221Bacillus cereusGene Names: blm
EC: 3.5.2.6
Find proteins for P04190 (Bacillus cereus)
Go to UniProtKB:  P04190
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.790α = 90.00
b = 61.980β = 93.67
c = 69.970γ = 90.00
Software Package:
Software NamePurpose
MADNESdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance