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

Christine Addy, Masato Ohara, Fumihiro Kawai, Akinori Kidera, Mitsunori Ikeguchi, Sotaro Fuchigami, Masanori Osawa, Ichio Shimada, Sam Yong Park, Jeremy R H Tame, Jonathan G. Heddle

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)221-229
Number of pages9
JournalActa Crystallographica Section D: Biological Crystallography
Volume63
Issue number2
DOIs
Publication statusPublished - 2007 Feb
Externally publishedYes

Fingerprint

Calorimetry
Crystallography
Nickel
crystallography
Spectrum Analysis
heat measurement
Binding Sites
nickel
Spectroscopy
spectroscopy
Crystal structure
crystal structure
Escherichia coli
Periplasmic Binding Proteins
proteins
mutagenesis
Mutagenesis
histidine
Poisons
respiration

Keywords

  • Nickel-binding proteins
  • NikA

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Condensed Matter Physics
  • Structural Biology

Cite this

Nickel binding to NikA : An additional binding site reconciles spectroscopy, calorimetry and crystallography. / Addy, Christine; Ohara, Masato; Kawai, Fumihiro; Kidera, Akinori; Ikeguchi, Mitsunori; Fuchigami, Sotaro; Osawa, Masanori; Shimada, Ichio; Park, Sam Yong; Tame, Jeremy R H; Heddle, Jonathan G.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 63, No. 2, 02.2007, p. 221-229.

Research output: Contribution to journalArticle

Addy, C, Ohara, M, Kawai, F, Kidera, A, Ikeguchi, M, Fuchigami, S, Osawa, M, Shimada, I, Park, SY, Tame, JRH & Heddle, JG 2007, 'Nickel binding to NikA: An additional binding site reconciles spectroscopy, calorimetry and crystallography', Acta Crystallographica Section D: Biological Crystallography, vol. 63, no. 2, pp. 221-229. https://doi.org/10.1107/S0907444906048712
Addy, Christine ; Ohara, Masato ; Kawai, Fumihiro ; Kidera, Akinori ; Ikeguchi, Mitsunori ; Fuchigami, Sotaro ; Osawa, Masanori ; Shimada, Ichio ; Park, Sam Yong ; Tame, Jeremy R H ; Heddle, Jonathan G. / Nickel binding to NikA : An additional binding site reconciles spectroscopy, calorimetry and crystallography. In: Acta Crystallographica Section D: Biological Crystallography. 2007 ; Vol. 63, No. 2. pp. 221-229.
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