Nickel coordination is regulated by the DNA-bound state of NikR

Paul E. Carrington, Peter T. Chivers, Faizah Al-Mjeni, Robert T. Sauer, Michael J. Maroney

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

The uptake of nickel in Escherichia coli and other microorganisms is transcriptionally regulated by the NikR repressor or its homologs. Here we report the structure of the high-affinity nickel-binding site in NikR and show that it responds dramatically to DNA binding. X-ray absorption spectroscopy reveals that nickel in the holo-NikR protein is bound in a novel four-coordinate planar site consisting of two histidines, one additional O- or N-donor ligand and one S-donor ligand. Site-directed mutation of His87, His89, Cys95 or Glu97 in NikR to alanine eliminates high-affinity nickel binding and abolishes DNA binding but maintains stable protein folding. An unanticipated feature of the NikR structure is that the nickel coordination responds to DNA binding. A six-coordinate nickel site composed of O- or N-donor ligands, but lacking cysteine, forms when NikR binds to operator DNA. Because nickel binding and DNA binding are mediated by different domains within NikR, a communication link between the two domains is implicated, consistent with the finding that the nickel-binding site in a fragment corresponding to the C-terminal domain of NikR is structurally distinct from that found in holo-NikR.

Original languageEnglish
Pages (from-to)126-130
Number of pages5
JournalNature Structural Biology
Volume10
Issue number2
DOIs
Publication statusPublished - Feb 1 2003

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Nickel
DNA
Ligands
X-Ray Absorption Spectroscopy
Binding Sites
Protein folding
X ray absorption spectroscopy
Protein Folding
Histidine
Alanine
Microorganisms
Escherichia coli
Telecommunication links
Cysteine
Mutation
Proteins

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Genetics

Cite this

Carrington, P. E., Chivers, P. T., Al-Mjeni, F., Sauer, R. T., & Maroney, M. J. (2003). Nickel coordination is regulated by the DNA-bound state of NikR. Nature Structural Biology, 10(2), 126-130. https://doi.org/10.1038/nsb890

Nickel coordination is regulated by the DNA-bound state of NikR. / Carrington, Paul E.; Chivers, Peter T.; Al-Mjeni, Faizah; Sauer, Robert T.; Maroney, Michael J.

In: Nature Structural Biology, Vol. 10, No. 2, 01.02.2003, p. 126-130.

Research output: Contribution to journalArticle

Carrington, PE, Chivers, PT, Al-Mjeni, F, Sauer, RT & Maroney, MJ 2003, 'Nickel coordination is regulated by the DNA-bound state of NikR', Nature Structural Biology, vol. 10, no. 2, pp. 126-130. https://doi.org/10.1038/nsb890
Carrington, Paul E. ; Chivers, Peter T. ; Al-Mjeni, Faizah ; Sauer, Robert T. ; Maroney, Michael J. / Nickel coordination is regulated by the DNA-bound state of NikR. In: Nature Structural Biology. 2003 ; Vol. 10, No. 2. pp. 126-130.
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