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Crystal structure of the nickel-responsive transcription factor NikR

Nature Structural & Molecular Biology volume 10, pages 794–799 (2003)Cite this article

Abstract

NikR is a metal-responsive transcription factor that controls nickel uptake in Escherichia coli by regulating expression of a nickel-specific ATP-binding cassette (ABC) transporter. We have determined the first two structures of NikR: the full-length apo repressor at a resolution of 2.3 Å and the nickel-bound C-terminal regulatory domain at a resolution of 1.4 Å. NikR is the only known metal-responsive member of the ribbon-helix-helix family of transcription factors, and its structure has a quaternary arrangement consisting of two dimeric DNA-binding domains separated by a tetrameric regulatory domain that binds nickel. The position of the C-terminal regulatory domain enforces a large spacing between the contacts that each NikR DNA-binding domain can make with the nik operator. The regulatory domain of NikR contains four nickel-binding sites at the tetramer interface, each exhibiting a novel square-planar coordination by three histidines and one cysteine side chain.

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Figure 1: NikR structures and structural comparisons.
Figure 2: Strictly conserved amino acids at the high-affinity nickel-binding site of NikR.
Figure 3: Side chain movements and interactions at the high-affinity nickel site.
Figure 4: NikR versus other ribbon-helix-helix transcription factors.

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Acknowledgements

This research is supported in part by the US National Institutes of Health (NIH) (R.T.S., C.L.D.), Searle Scholars Program (C.L.D.), Cecil and Ida Green Career Development Fund (C.L.D.), Lester Wolfe Predoctoral Fellowship (E.R.S.), and the Gray Fund for Undergraduate Research (Y.G.). Data were collected at the National Synchrotron Light Source (NSLS), Advanced Light Source (ALS), Advanced Photon Source (APS), and Stanford Synchrotron Radiation Laboratory (SSRL) synchrotrons. Synchrotron facilities are funded by the US Department of Energy (ALS 5.0.2, NSLS X25, SSRL), NIH National Center of Research Resources (APS NE-CAT 8BM, NSLS X25), and the US National Institute of General Medical Sciences (NSLS X25).

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  1. Peter T Chivers

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

Authors and Affiliations

  1. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Eric R Schreiter, Michael D Sintchak, Yayi Guo & Catherine L Drennan

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

    Peter T Chivers & Robert T Sauer

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Correspondence to Catherine L Drennan.

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Schreiter, E., Sintchak, M., Guo, Y. et al. Crystal structure of the nickel-responsive transcription factor NikR. Nat Struct Mol Biol 10, 794–799 (2003). https://doi.org/10.1038/nsb985

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