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
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
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
Similar content being viewed by others
Accession codes
References
Holtz, J.K. & Topal, M.D. J. Biol. Chem. 269, 27286–27290 (1994).
Jo, K. & Topal, M.D. Science 267, 1817–1820 (1995).
Conrad, M. & Topal, M.D. Proc. Natl. Acad. Sci. USA 86, 9707–9711 (1989).
Yang, C.C. & Topal, M.D. Biochemistry 31, 9657–9664 (1992).
Topal, M.D., Thresher, R.J., Conrad, M. & Griffith, J. Biochemistry 30, 2007–2010 (1991).
Huai, Q. et al. EMBO J. 19, 3110–3118 (2000).
Colandene, J.D. & Topal, M.D. Biochemistry 39, 13703–13707 (2000).
Kovall, R.A. & Matthews, B.W. Curr. Opin. Chem. Biol. 3, 578–583 (1999).
Harrison, S.C. Nature 353, 715–719 (1991).
Pabo, C.O. & Sauer, R.T. Annu. Rev. Biochem. 61, 1053–1095 (1992).
Nelson, H.C.M. Curr. Opin. Genet. Dev. 5, 180–189 (1995).
Berger, J.M., Fass, D., Wang, J.C. & Harrison, S.C. Proc. Natl. Acad. Sci. USA 95, 7876–7881 (1998).
Rosenberg, L.M. Curr. Opin. Struct. Biol. 1, 104–113 (1991).
Winkler, F.K. et al. EMBO J. 12, 1781–1795 (1993).
Newman, M. et al. EMBO J. 17, 5466–5476 (1998).
Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V. & Huber, R. EMBO J. 18, 5805–5816 (1999).
Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I. & Aggarwal, A.K Science 269, 656–663 (1995).
Cheng, X., Balendiran, K., Schildkraut, I. & Anderson, J.E. EMBO J. 17, 3927–3935 (1994).
Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V. & Huber, R. Nature Struct. Biol. 7, 792–799 (2000).
Yang, C.C., Baxter, B.K. & Topal, M.D. Biochemistry 33, 14918–14925 (1994).
Colandene, J.D. & Topal, M.D. Proc. Natl. Acad. Sci. USA 95, 3531–3536 (1998).
Keck, J.L. & Berger, J.M. Nature Struct. Biol. 6, 900–902 (1999).
Gopaul, D.N. & Van Duyne, G.D. Curr. Opin. Struct. Biol. 9, 14–20 (1999).
Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 (1997).
Navaza, J. & Saludjian, P. Methods Enzymol. 276, 581–594 (1997).
Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgard, M. Acta Crystallogr. A 47, 110–119 (1991).
Brünger, A.T. et al. Acta Crystallogr. D 54, 905–921 (1998).
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
Corresponding authors
Rights 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
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/90366
This article is cited by
-
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes
BMC Bioinformatics (2012)
-
Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis
JBIC Journal of Biological Inorganic Chemistry (2007)
-
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
BMC Bioinformatics (2005)