1DXK

Metallo-beta-lactamase from Bacillus cereus 569/H/9 C168S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase.

Chantalat, L.Duee, E.Galleni, M.Frere, J.M.Dideberg, O.

(2000) Protein Sci 9: 1402-1406

  • DOI: 10.1110/ps.9.7.1402
  • Primary Citation of Related Structures:  
    1DXK

  • PubMed Abstract: 
  • Beta-lactamases are involved in bacterial resistance. Members of the metallo-enzyme class are now found in many pathogenic bacteria and are becoming thus of major clinical importance. Despite the availability of Zn-beta-lactamase X-ray structures their mechanism of action is still unclear ...

    Beta-lactamases are involved in bacterial resistance. Members of the metallo-enzyme class are now found in many pathogenic bacteria and are becoming thus of major clinical importance. Despite the availability of Zn-beta-lactamase X-ray structures their mechanism of action is still unclear. One puzzling observation is the presence of one or two zincs in the active site. To aid in assessing the role of zinc content in beta-lactam hydrolysis, the replacement by Ser of the zinc-liganding residue Cys168 in the Zn-beta-lactamase from Bacillus cereus strain 569/H/9 was carried out: the mutant enzyme (C168S) is inactive in the mono-Zn form, but active in the di-Zn form. The structure of the mono-Zn form of the C168S mutant has been determined at 1.85 A resolution. Ser168 occupies the same position as Cys168 in the wild-type enzyme. The protein residues mostly affected by the mutation are Asp90-Arg91 and His210. A critical factor for the activity of the mono-Zn species is the distance between Asp90 and the Zn ion, which is controlled by Arg91: a slight movement of Asp90 impairs catalysis. The evolution of a large superfamily including Zn-beta-lactamases suggests that they may not all share the same mechanism.


    Related Citations: 
    • 1.85 A Resolution Structure of the Zinc(II) Beta-Lactamase from Bacillus Cereus
      Carfi, A., Duee, E., Galleni, M., Frere, J.M., Dideberg, O.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 313
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CLASS B BETA-LACTAMASEA227Bacillus cereusMutation(s): 1 
Gene Names: blm
EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus)
Explore P04190 
Go to UniProtKB:  P04190
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
C [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.79α = 90
b = 61.25β = 92.93
c = 69.28γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-25
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Derived calculations, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Source and taxonomy
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references