Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 5.8

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Evidence of adaptability in metal coordination geometry and active-site loop conformation among B1 metallo-beta-lactamases .

Gonzalez, J.M.Buschiazzo, A.Vila, A.J.

(2010) Biochemistry 49: 7930-7938

  • DOI: https://doi.org/10.1021/bi100894r
  • Primary Citation of Related Structures:  
    3I0V, 3I11, 3I13, 3I14, 3I15

  • PubMed Abstract: 

    Subclass B1 beta-lactamases are Zn(II)-dependent hydrolases that confer bacterial resistance to most clinically useful beta-lactam antibiotics. The enzyme BcII from Bacillus cereus is a prototypical enzyme that belongs to this group, the first Zn(II)-dependent beta-lactamase to be discovered. Crucial aspects of the BcII catalytic mechanism and metal binding mode have been assessed mostly on the Co(II)-substituted surrogate. Here we report a high-resolution structure of Co(II)-BcII, revealing a metal coordination geometry identical to that of the native zinc enzyme. In addition, a high-resolution structure of the apoenzyme, together with structures with different degrees of metal occupancy and oxidation levels of a conserved Cys ligand, discloses a considerable mobility of two loops containing four metal ligands (namely, regions His116-Arg121 and Gly219-Cys221). This flexibility is expected to assist in the structural rearrangement of the metal sites during catalytic turnover, which, along with the coordination geometry adaptability of Zn(II) ions, grants the interaction with a variety of substrates, a characteristic feature of B1 metallo-beta-lactamases.

  • Organizational Affiliation

    Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, S2002LRK Rosario, Argentina.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase 2227Bacillus cereusMutation(s): 0 
Find proteins for P04190 (Bacillus cereus)
Explore P04190 
Go to UniProtKB:  P04190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04190
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.111α = 90
b = 61.41β = 93.06
c = 69.483γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations