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Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding

Nature volume 403, pages 916–921 (2000)Cite this article

Abstract

Regulatory factor X (RFX) proteins are transcriptional activators that recognize X-boxes (DNA of the sequence 5′-GTNRCC(0–3N)RGYAAC-3′, where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD). DNA-binding defects in the protein RFX5 cause bare lymphocyte syndrome or major histocompatibility antigen class II deficiency1. RFX1, -2 and -3 regulate expression of other medically important gene products (for example, interleukin-5 receptor α chain, IL-5Rα)2. Fusions of the ligand-binding domain of the oestrogen receptor with the DBD of RFX4 occur in some human breast tumours3. Here we present a 1.5 Å-resolution structure of two copies of the DBD of human RFX1 (hRFX1) binding cooperatively to a symmetrical X-box4,5. hRFX1 is an unusual member of the winged-helix subfamily of helix–turn–helix proteins6 because it uses a β-hairpin (or wing) to recognize DNA instead of the recognition helix typical of helix–turn–helix proteins. A new model for interactions between linker histones and DNA is proposed.

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Figure 1: Protein and oligonucleotide sequences.
Figure 2: RFX1 and HNF-3γ DBDs.
Figure 3: Protein–DNA interactions.
Figure 4: Model for linker histone–DNA interactions.

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Acknowledgements

We thank D. Thiel and the MacCHESS staff, and Z. Dauter and K.R. Rajashankar and the NSLS X9B staff for help with X-ray data collection. We thank C. Lenoir for assistance in peptide synthesis, and J. Bonanno, K. L. Clark, J. E. Darnell, R. C. Deo, D. Jeruzalmi, J. Kuriyan, E. Lai, H. A. Lewis, S. K. Nair and G. A. Petsko for many useful discussions. S.K.B. is an Investigator in the Howard Hughes Medical Institute. This work was supported by the National Institute of General Medical Sciences.

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Authors and Affiliations

  1. Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology,

    Ketan S. Gajiwala, Hua Chen & Stephen K. Burley

  2. Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue,, New York, 10021, New York, USA

    Hua Chen & Stephen K. Burley

  3. Départment de Pharmacologie Moléculaire et Structurale, INSERM U266, CNRS URA D1500, UFR des Sciences Pharmaceutiques et Bioligiques, 4 Avenue de l’Observatoire , Paris, Cedex 06 75720, France

    Fabrice Cornille & Bernard P. Roques

  4. Départment de Génétique et Microbiologie, Centre Médical Universitaire (CMU), 1, rue Michel-Servet, Genéve, 4, CH 1211, Switzerland

    Walter Reith & Bernard Mach

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  1. Ketan S. Gajiwala
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Correspondence to Stephen K. Burley.

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Gajiwala, K., Chen, H., Cornille, F. et al. Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature 403, 916–921 (2000). https://doi.org/10.1038/35002634

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