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: 2.67). 03/2007; 63(Pt 2):221-9. DOI: 10.1107/S0907444906048712
Source: PubMed


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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    • "This result also applied to the structure determined by Heddle and collaborators. Indeed, in 2007, these authors revised their NikA structure and agreed with our previous interpretation [16]. Therefore, all these studies suggested the existence of a EDTA-like natural chelator involved in nickel binding. "
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    ABSTRACT: Escherichia coli require nickel for the synthesis of [NiFe] hydrogenases under anaerobic growth conditions. Nickel import depends on the specific ABC-transporter NikABCDE encoded by the nik operon, which deletion causes the complete abolition of hydrogenase activity. We have previously postulated that the periplasmic binding protein NikA binds a natural metallophore containing three carboxylate functions that coordinate a Ni(II) ion, the fourth ligand being His416, the only direct metal-protein contact, completing a square-planar coordination for the metal. The crystal structure of the H416I mutant showed no electron density corresponding to a metal-chelator complex. In vivo experiments indicate that the mutation causes a significant decrease in nickel uptake and hydrogenase activity. These results confirm the essential role of His416 in nickel transport by NikA.
    FEBS letters 02/2011; 585(4):711-5. DOI:10.1016/j.febslet.2011.01.038 · 3.17 Impact Factor
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    • "Cherrier et al. suggested that NikA binds Ni chelated by a small organic molecule, such as butane-1,2,4-tricarboxylate (BTC), and that some residues, including Tyr402, Arg137, Arg97 and His416, form a binding site that is involved in the BTC-Ni-NikA interaction [78]. On the other hand, Addy and coworkers showed that Ni may bind E. coli NikA without chelators and is bound to two histidine residues (His56 and His442, although not conserved in other NikA proteins) at a position distant from the previously characterized binding site [79]. Here, the presence of the majority of these residues was used to help predict NikA proteins. "
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