Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

A new family of plant transcription factors displays a novel ssDNA-binding surface

Nature Structural Biology volume 9, pages 512–517 (2002)Cite this article

Abstract

The crystal structure of p24, the single-stranded DNA (ssDNA) binding subunit of the plant defense transcription factor PBF-2, has been determined to 2.3 Å resolution. p24 is representative of a novel family of ubiquitous plant-specific proteins that we refer to as the Whirly family because of their quaternary structure. PBF-2 is composed of four p24 molecules that interact through a helix-loop-helix motif. This interaction produces a central pore, with β-strands radiating outwards, resulting in a whirligig appearance to the quaternary structure. The noncrystallographic C4 symmetry arrangement of p24 subunits is novel for ssDNA binding proteins and may explain the binding specificity of PBF-2. This structural arrangement also supports the role of PBF-2 in binding melted promoter regions to modulate gene expression.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Three-dimensional structure of PBF-2.
Figure 2: Structural conservation of Whirly proteins.
Figure 3: PBF-2 binds one ssDNA molecule in vitro.
Figure 4: Identification of the KGKAAL sequence critical for p24 ssDNA binding activity and model of PBF-2 binding to melted dsDNA.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Brivanlou, A.H. & Darnell, J.E., Jr Science 295, 813–818 (2002).

    Article  CAS  Google Scholar 

  2. Roeder, R.G. Trends Biochem. Sci. 21, 327–335 (1996).

    Article  CAS  Google Scholar 

  3. Kornberg, R.D. Trends Cell. Biol. 9, M46–49 (1999).

    Article  CAS  Google Scholar 

  4. Woychik, N.A. & Hampsey, M. Cell 108, 453–463 (2002).

    Article  CAS  Google Scholar 

  5. Nikolov, D.B. et al. Nature 360, 40–46 (1992).

    Article  CAS  Google Scholar 

  6. Rushton, P. & Somssich, E. Curr. Opin. Plant Biol. 1, 311–315 (1998).

    Article  CAS  Google Scholar 

  7. Maleck, K. et al. Nature Genet. 26, 403–410 (2000).

    Article  CAS  Google Scholar 

  8. Matton, D.P. & Brisson, N. Mol. Plant Microbe Interact. 2, 325–331 (1989).

    Article  CAS  Google Scholar 

  9. Matton, D.P., Prescott, G., Bertrand, C., Camirand, A. & Brisson, N. Plant Mol. Biol. 22, 279–291 (1993).

    Article  CAS  Google Scholar 

  10. Després, C., Subramaniam, R., Matton, D.P. & Brisson, N. Plant Cell 7, 589–598 (1995).

    Article  Google Scholar 

  11. Desveaux, D, Després, C., Joyeux, A., Subramaniam, R. & Brisson, N. Plant Cell 12, 1477–1489 (2000).

    Article  CAS  Google Scholar 

  12. Hendrickson, W. & Ogata, C. Methods Enzymol. 276, 494–523 (1997).

    Article  CAS  Google Scholar 

  13. Desveaux, D., Allard, J., Brisson, N. & Sygusch, J. Acta Crystallogr. D 58, 296–298 (2002).

    Article  Google Scholar 

  14. Raghunathan, S., Ricard, C.S., Lohman, T.M. & Waksman, G. Proc. Natl. Acad. Sci. USA 94, 6652–6657 (1997).

    Article  CAS  Google Scholar 

  15. Yang, C., Curth, U., Urbanke, C. & Kang, C. Nature Struct. Biol. 4, 153–157 (1997).

    Article  CAS  Google Scholar 

  16. Rost, B. & Sander, C. J. Mol. Biol. 232, 584–599 (1993).

    Article  CAS  Google Scholar 

  17. Rost, B. & Sander, C. Proteins 19, 55–72 (1994).

    Article  CAS  Google Scholar 

  18. Holm, L. & Sander, C. J. Mol. Biol. 233, 123–138 (1993).

    Article  CAS  Google Scholar 

  19. Werten, S., Wechselberger, R., Boelens, R., van der Vliet, P.C. & Kaptein, R. J. Biol. Chem. 274, 3693–3699 (1999).

    Article  CAS  Google Scholar 

  20. Brandsen, J. et al. Nature Struct. Biol. 4, 900–903 (1997).

    Article  CAS  Google Scholar 

  21. Bates, A.D. & Maxwell, A. In DNA Topology (eds Rickwood, D. & Male, D.) 88–95 (IRL Press, Oxford; 1993).

    Google Scholar 

  22. Duncan, R. et al. Genes Dev. 8, 465–480 (1994).

    Article  CAS  Google Scholar 

  23. Kowalski, D., Natale, D.A. & Eddy, M.J. Proc. Natl. Acad. Sci. USA 85, 9464–9468 (1988).

    Article  CAS  Google Scholar 

  24. Gerber, H.-P. et al. Science 263, 808–811 (1994).

    Article  CAS  Google Scholar 

  25. Kahn, J.D., Yun, E. & Crothers, D.M. Nature 368, 163–166 (1994).

    Article  CAS  Google Scholar 

  26. Travers, A. & Muskhelishvili, G. J. Mol. Biol. 279, 1027–1043 (1998).

    Article  CAS  Google Scholar 

  27. Suck, D. Nature Struct. Biol. 4, 161–165 (1997).

    Article  CAS  Google Scholar 

  28. Bochkarev, A., Pfuetzner, R.A., Edwards, A.M. & Frappier, L. Nature 385, 176–181 (1997).

    Article  CAS  Google Scholar 

  29. Ruff, M. et al. Science 252, 1682–1689 (1991).

    Article  CAS  Google Scholar 

  30. Klinge, C.M. Nucleic Acids Res. 29, 2905–2919 (2001).

    Article  CAS  Google Scholar 

  31. Terwilliger, T.C. & Berendzen, J. Acta Crystallogr. D 55, 849–861 (1999).

    Article  CAS  Google Scholar 

  32. Brünger, A.T. et al. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  33. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  34. Diamond, R. Protein Sci. 1, 1279–1287 (1992).

    Article  CAS  Google Scholar 

  35. Constable, C.P. & Brisson, N. Planta 188, 289–295 (1992).

    Google Scholar 

  36. Thompson, J.D., Higgins, D.G. & Gibson, T.J. Nucleic Acids Res. 22, 4673–4680 (1994).

    Article  CAS  Google Scholar 

  37. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  38. Luzzati, P.V. Acta Crystallogr. 5, 802–810 (1952).

    Article  Google Scholar 

Download references

Acknowledgements

The assistance of T.-S. Yoon in data collection and reduction is gratefully acknowledged. Research carried out at the National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the U.S. Department of Energy, Division of Materials Sciences and Division of Chemical Sciences. Assistance by X8-C and X25 beamline personnel is gratefully appreciated. This research was supported by a fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) to D.D. and research grants from the Canadian Institutes of Health Research to J.S., from NSERC to both N.B. and J.S. and the Fonds pour la Formation de Chercheurs et l'Aide à la Recherche, Québec to N.B.

Author information

Author notes

  1. Darrell Desveaux and Julie Allard: These authors contributed equally to this research.

Authors and Affiliations

  1. Department of Biochemistry, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, H3C 3J7, Québec, Canada

    Darrell Desveaux, Julie Allard, Normand Brisson & Jurgen Sygusch

Authors
  1. Darrell Desveaux
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Julie Allard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Normand Brisson
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jurgen Sygusch
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Normand Brisson or Jurgen Sygusch.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Desveaux, D., Allard, J., Brisson, N. et al. A new family of plant transcription factors displays a novel ssDNA-binding surface. Nat Struct Mol Biol 9, 512–517 (2002). https://doi.org/10.1038/nsb814

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb814

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing