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

Nature Structural Biology volume 10, pages 126–130 (2003)Cite this article

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.

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Figure 1: Ni K-edge XANES spectra of E. coli NikR samples.
Figure 2: Unfiltered k3-weighted EXAFS data and fits from Table 1.
Figure 3: High-affinity nickel-binding motif in the C-domain of NikR.

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Acknowledgements

The authors acknowledge support from the Donors of The Petroleum Research Fund, administered by the American Chemical Society, the University of Massachusetts (M.J.M.) and the National Institutes of Health (R.T.S.). The National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory is supported by the U.S. Department of Energy, Division of Materials Sciences and Division of Chemical Sciences. Beamline X9B at NSLS is supported in part by the NIH.

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Author notes

  1. Peter T. Chivers

    Present address: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA

  2. Faizah Al-Mjeni

    Present address: Department of Chemistry, Sultan Qaboos University, P.O. Box 36, Al-Khod, PC 123, Sultanate of Oman

Authors and Affiliations

  1. Department of Chemistry, University of Massachusetts, Amherst, 01003-9336, Massachusetts, USA

    Paul E. Carrington, Faizah Al-Mjeni & Michael J. Maroney

  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Peter T. Chivers & Robert T. Sauer

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Correspondence to Michael J. Maroney.

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Carrington, P., Chivers, P., Al-Mjeni, F. et al. Nickel coordination is regulated by the DNA-bound state of NikR. Nat Struct Mol Biol 10, 126–130 (2003). https://doi.org/10.1038/nsb890

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