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:

Structure of NaeI–DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement

Abstract

NaeI, a novel DNA endonuclease, shows topoisomerase and recombinase activities when a Lys residue is substituted for Leu 43. The NaeI–DNA structure demonstrates that each of the two domains of NaeI recognizes one molecule of DNA duplex. DNA recognition induces dramatic rearrangements: narrowing the binding site of the Topo domain 16 Å to grip DNA, widening that of the Endo domain 8 Å to encircle and bend DNA 45° for cleavage, and completely rebuilding the homodimer interface. The NaeI–DNA structure presents the first example of novel recognition of two copies of one DNA sequence by two different amino acid sequences and two different structural motifs in one polypeptide.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Dimeric structure of NaeI–DNA complex.
Figure 2: DNA binding.
Figure 3: Stereo view of conformational change of NaeI upon DNA binding.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Holtz, J.K. & Topal, M.D. J. Biol. Chem. 269, 27286–27290 (1994).

    CAS  PubMed  Google Scholar 

  2. Jo, K. & Topal, M.D. Science 267, 1817–1820 (1995).

    Article  CAS  Google Scholar 

  3. Conrad, M. & Topal, M.D. Proc. Natl. Acad. Sci. USA 86, 9707–9711 (1989).

    Article  CAS  Google Scholar 

  4. Yang, C.C. & Topal, M.D. Biochemistry 31, 9657–9664 (1992).

    Article  CAS  Google Scholar 

  5. Topal, M.D., Thresher, R.J., Conrad, M. & Griffith, J. Biochemistry 30, 2007–2010 (1991).

    Article  Google Scholar 

  6. Huai, Q. et al. EMBO J. 19, 3110–3118 (2000).

    Article  CAS  Google Scholar 

  7. Colandene, J.D. & Topal, M.D. Biochemistry 39, 13703–13707 (2000).

    Article  CAS  Google Scholar 

  8. Kovall, R.A. & Matthews, B.W. Curr. Opin. Chem. Biol. 3, 578–583 (1999).

    Article  CAS  Google Scholar 

  9. Harrison, S.C. Nature 353, 715–719 (1991).

    Article  CAS  Google Scholar 

  10. Pabo, C.O. & Sauer, R.T. Annu. Rev. Biochem. 61, 1053–1095 (1992).

    Article  CAS  Google Scholar 

  11. Nelson, H.C.M. Curr. Opin. Genet. Dev. 5, 180–189 (1995).

    Article  CAS  Google Scholar 

  12. Berger, J.M., Fass, D., Wang, J.C. & Harrison, S.C. Proc. Natl. Acad. Sci. USA 95, 7876–7881 (1998).

    Article  CAS  Google Scholar 

  13. Rosenberg, L.M. Curr. Opin. Struct. Biol. 1, 104–113 (1991).

    Article  CAS  Google Scholar 

  14. Winkler, F.K. et al. EMBO J. 12, 1781–1795 (1993).

    Article  CAS  Google Scholar 

  15. Newman, M. et al. EMBO J. 17, 5466–5476 (1998).

    Article  CAS  Google Scholar 

  16. Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V. & Huber, R. EMBO J. 18, 5805–5816 (1999).

    Article  CAS  Google Scholar 

  17. Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I. & Aggarwal, A.K Science 269, 656–663 (1995).

    Article  CAS  Google Scholar 

  18. Cheng, X., Balendiran, K., Schildkraut, I. & Anderson, J.E. EMBO J. 17, 3927–3935 (1994).

    Article  Google Scholar 

  19. Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V. & Huber, R. Nature Struct. Biol. 7, 792–799 (2000).

    Article  CAS  Google Scholar 

  20. Yang, C.C., Baxter, B.K. & Topal, M.D. Biochemistry 33, 14918–14925 (1994).

    Article  CAS  Google Scholar 

  21. Colandene, J.D. & Topal, M.D. Proc. Natl. Acad. Sci. USA 95, 3531–3536 (1998).

    Article  CAS  Google Scholar 

  22. Keck, J.L. & Berger, J.M. Nature Struct. Biol. 6, 900–902 (1999).

    Article  CAS  Google Scholar 

  23. Gopaul, D.N. & Van Duyne, G.D. Curr. Opin. Struct. Biol. 9, 14–20 (1999).

    Article  CAS  Google Scholar 

  24. Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  25. Navaza, J. & Saludjian, P. Methods Enzymol. 276, 581–594 (1997).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

Download references

Acknowledgements

We thank R. Sweet for help with data collection at beamline X12C in the National Synchrotron Light Source. This research is partially supported by the NIH.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Michael D. Topal or Hengming Ke.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Huai, Q., Colandene, J., Topal, M. et al. Structure of NaeI–DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Mol Biol 8, 665–669 (2001). https://doi.org/10.1038/90366

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/90366

This article is cited by

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