2BG8

Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH4.5 using 20 Micromolar ZnSO4 in the buffer. 1mM DTT and 1mM TCEP-HCl were used as reducing agents.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Effect of Ph on the Active Site of an Arg121Cys Mutant of the Metallo-Beta-Lactamase from Bacillus Cereus: Implications for the Enzyme Mechanism

Davies, A.M.Rasia, R.M.Vila, A.J.Sutton, B.J.Fabiane, S.M.

(2005) Biochemistry 44: 4841

  • DOI: 10.1021/bi047709t
  • Primary Citation of Related Structures:  
    2BFL, 2BFK, 2BG6, 2BG2, 2BFZ, 2BG8, 2BG7, 2BGA

  • PubMed Abstract: 
  • The zinc-dependent metallo-beta-lactamases are a group of bacterial enzymes that pose a threat to the future efficacy of present-day antibiotics. Their mechanism is poorly understood, and there are no clinically useful inhibitors. While most members of the group contain two tightly bound zinc ions in their active sites, the Bacillus cereus enzyme has a much lower affinity for its second zinc (Zn2), thought to be due to the presence of Arg121 immediately beneath the floor of the active site (cf ...

    The zinc-dependent metallo-beta-lactamases are a group of bacterial enzymes that pose a threat to the future efficacy of present-day antibiotics. Their mechanism is poorly understood, and there are no clinically useful inhibitors. While most members of the group contain two tightly bound zinc ions in their active sites, the Bacillus cereus enzyme has a much lower affinity for its second zinc (Zn2), thought to be due to the presence of Arg121 immediately beneath the floor of the active site (cf. Cys/Ser/His121 in the bizinc enzymes). Crystal structures of the Arg121Cys mutant of the B. cereus 569/H/9 enzyme were solved at pH 7.0, 5.0, and 4.5, each in the presence of either 20 microM or 20 mM Zn(2+) to generate the mono- and bizinc forms, respectively. Surprisingly, the structure of the active site was unaffected by the mutation; a network of ordered water molecules replaced the interactions made by the arginine side chain, and the occupancy of Zn2 appeared minimally changed. As the pH was lowered, Zn2 moved away from one of its ligands, Asp120, but was "tracked" by two others, Cys221 and His263. Furthermore, the hydroxide ion (and proposed nucleophile for beta-lactam hydrolysis) was bound to Zn1 at pH 5 and above but absent at pH 4.5. This provides experimental evidence for an earlier proposed mechanism in which protonation of Asp120 and the Zn1-bound hydroxide are the two events that lead to the loss of activity at low pH.


    Related Citations: 
    • Exploring the Role and Binding Affinity of a Second Zinc Equivalent in B. Cereus Metallo-Beta-Lactamase
      Rasia, R.M., Vila, A.J.
      (2002) Biochemistry 41: 1853
    • Crystal Structure of the Zinc-Dependent Beta-Lactamase from Bacillus Cereus at 1.9A Resolution: Binuclear Active Site with Features of a Mononuclear Enzyme
      Fabiane, S.M., Sohi, M.K., Wan, T., Payne, D.J., Bateson, J.H., Mitchell, T., Sutton, B.J.
      (1998) Biochemistry 37: 12404

    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London Bridge, SE1 1UL, London, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-LACTAMASE IIA227Bacillus 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-LACTAMASE IIB227Bacillus 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A] , J [auth A] , K [auth A] , L [auth A] , U [auth B] , V [auth B] , W [auth B] , X [auth B] , 
I [auth A],  J [auth A],  K [auth A],  L [auth A],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , M [auth A] , N [auth A] , O [auth B] , 
C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  M [auth A],  N [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A], T [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.25α = 90
b = 67.25β = 90
c = 177.8γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Changes: Data collection, Experimental preparation