Article

Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.

Graduate School of Integrated Science, Yokohama City University, Tsurumi, Suehiro 1-7-29, Yokohama 230-0045, Japan.
Acta Crystallographica Section D Biological Crystallography (impact factor: 12.62). 03/2007; 63(Pt 2):221-9. DOI:10.1107/S0907444906048712
Source: PubMed

ABSTRACT Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.

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Keywords

anaerobic respiration
 
apo form
 
binding-site mutant
 
characterized binding site
 
crystal structures
 
disruptive mutations
 
E. coli encodes
 
export systems
 
extensive mutagenesis
 
Intracellular nickel
 
isothermal titration calorimetry
 
known nickel-binding site
 
large numbers
 
nickel affinity
 
nickel-uptake system
 
novel site
 
periplasmic nickel-binding protein NikA
 
two binding sites
 
unusual nickel coordination
 
X-ray spectroscopic studies