4F6H

Mutagenesis of zinc ligand residue Cys221 reveals plasticity in the IMP-1 metallo-b-lactamase active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.744 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


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Literature

Mutagenesis of zinc ligand residue Cys221 reveals plasticity in the IMP-1 metallo-beta-lactamase active site

Horton, L.B.Shanker, S.Mikulski, R.Brown, N.G.Phillips, K.J.Lykissa, E.Venkataram Prasad, B.V.Palzkill, T.

(2012) Antimicrob.Agents Chemother. 56: 5667-5677

  • DOI: 10.1128/AAC.01276-12
  • Primary Citation of Related Structures:  4F6Z

  • PubMed Abstract: 
  • Metallo-β-lactamases catalyze the hydrolysis of a broad range of β-lactam antibiotics and are a concern for the spread of drug resistance. To analyze the determinants of enzyme structure and function, the sequence requirements for the subclass B1 IMP ...

    Metallo-β-lactamases catalyze the hydrolysis of a broad range of β-lactam antibiotics and are a concern for the spread of drug resistance. To analyze the determinants of enzyme structure and function, the sequence requirements for the subclass B1 IMP-1 β-lactamase zinc binding residue Cys221 were tested by saturation mutagenesis and evaluated for protein expression, as well as hydrolysis of β-lactam substrates. The results indicated that most substitutions at position 221 destabilized the enzyme. Only the enzymes containing C221D and C221G substitutions were expressed well in Escherichia coli and exhibited catalytic activity toward β-lactam antibiotics. Despite the lack of a metal-chelating group at position 221, the C221G enzyme exhibited high levels of catalytic activity in the presence of exogenous zinc. Molecular modeling suggests the glycine substitution is unique among substitutions in that the complete removal of the cysteine side chain allows space for a water molecule to replace the thiol and coordinate zinc at the Zn2 zinc binding site to restore function. Multiple methods were used to estimate the C221G Zn2 binding constant to be 17 to 43 μM. Studies of enzyme function in vivo in E. coli grown on minimal medium showed that both IMP-1 and the C221G mutant exhibited compromised activity when zinc availability was low. Finally, substitutions at residue 121, which is the IMP-1 equivalent of the subclass B3 zinc-chelating position, failed to rescue C221G function, suggesting the coordination schemes of subclasses B1 and B3 are not interchangeable.


    Organizational Affiliation

    Departments of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
236Pseudomonas aeruginosaGene Names: blaIMP-1 (bla IMP, bla-imp, blaESP, imp)
EC: 3.5.2.6
Find proteins for Q79MP6 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q79MP6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.744 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.016α = 90.00
b = 60.499β = 90.00
c = 84.287γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release