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.

Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I

Nature volume 367, pages 138–146 (1994)Cite this article

Abstract

The three-dimensional structure of the 67K amino-terminal fragment of Escherichia coli DNA topoisomerase I has been determined to 2.2 Å resolution. The polypeptide folds in an unusual way to give four distinct domains enclosing a hole large enough to accommodate a double-stranded DNA. The active-site tyrosyl residue, which is involved in the transient breakage of a DNA strand and the formation of a covalent enzyme–DNA intermediate, is present at the interface of two domains. The structure suggests a plausible mechanism by which E. coli DNA topoisomerase I and other members of the same DNA topoisomerase subfamily could catalyse the passage of one DNA strand through a transient break in another strand.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

Buy

All prices are NET prices.

References

  1. Gellert, M. A. Rev. Biochem. 50, 879–910 (1981).

    CAS  Article  Google Scholar 

  2. Wang, J. C. A. Rev. Biochem. 54, 665–697 (1985).

    CAS  Article  Google Scholar 

  3. Wang, J. C. J. biol. Chem. 266, 6659–6662 (1991).

    CAS  PubMed  Google Scholar 

  4. Proc. Int. Symp. on DNA Topoisomerases in ChemotherapyNagoya Japan (eds Anhoh, T., Ikeda, H. & Oguro, M.) (CRC, Florida, 1993).

  5. Liu, L. F. A. Rev. Biochem 58, 351–375 (1989).

    CAS  Article  Google Scholar 

  6. Drlica, K. & Franco, R. J. Biochemistry 27, 2253–2259 (1988).

    CAS  Article  Google Scholar 

  7. Wang, J. C. J. molec. Biol. 55, 523–533 (1971).

    CAS  Article  Google Scholar 

  8. Dean, F. et al. Cold Spring Harbor Symp. quant. Biol. 47, 769–777 (1982).

    CAS  Article  Google Scholar 

  9. DiGate, R. J. & Marians, K. J. J. biol. Chem. 264, 17924–17930 (1989).

    CAS  PubMed  Google Scholar 

  10. Wallis, J. W., Chrebet, G., Brodsky, G., Rolfe, M. & Rothstein, R. Cell 58, 409–419 (1989).

    CAS  Article  Google Scholar 

  11. Kim, R. A. & Wang, J. C. J. biol. Chem. 267, 17178–17185 (1992).

    CAS  PubMed  Google Scholar 

  12. Kikuchi, A. & Asai, K. Nature 309, 677–681 (1984).

    ADS  CAS  Article  Google Scholar 

  13. Confalonieri, F. et al. Proc. natn. Acad. Sci. U.S.A. 90, 4753–4757 (1993).

    ADS  CAS  Article  Google Scholar 

  14. Wang, J. C. in Nucleases (eds Roberts, R. & Linn, S.) 41–57 (Cold Spring Harbor Laboratory, New York, 1982).

    Google Scholar 

  15. Kornberg, A. & Baker, T. DNA Replication (Freeman, New York, 1992).

    Google Scholar 

  16. Tse-Dinh, Y.-C. & Beran-Steed, R. K. J. biol. Chem. 263, 15857–15859 (1988).

    CAS  PubMed  Google Scholar 

  17. Lynn, R. & Wang, J. C. Prot. Struct. Func. Genet. 6, 231–239 (1989).

    CAS  Article  Google Scholar 

  18. Tse-Dinh, Y.-C. J. biol. Chem. 266, 14217–14320 (1991).

    Google Scholar 

  19. Lima, C. D., Wang, J. C. & Mondragón, A. J. molec. Biol. 232, 1213–1216 (1993).

    CAS  Article  Google Scholar 

  20. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Acta. crystallogr. A47, 110–119 (1991).

    Article  Google Scholar 

  21. Hendrickson, W. A. & Konnert, J. H. in Biomolecular Structural, Function, Conformation and Evolution Vol. I (ed. Srinivisan, R.) 43–57 (Pergamon, Oxford, 1980).

    Google Scholar 

  22. Brunger, A. T., Kuriyan, J. & Karplus, M. Science 235, 458–460 (1987).

    ADS  CAS  Article  Google Scholar 

  23. Brunger, A. T. Nature 355, 472–474 (1992).

    ADS  CAS  Article  Google Scholar 

  24. Hodel, A., Kim, S.-H. & Brunger, A. T. Acta crystallogr. A48, 851–858 (1992).

    Article  Google Scholar 

  25. Bränden, C.-I. Quart. Rev. Biophys. 13, 317–338 (1980).

    Article  Google Scholar 

  26. Beese, L. S. & Steitz, T. A. EMBO J. 10, 25–33 (1991).

    CAS  Article  Google Scholar 

  27. Domanico, P. L. & Tse-Dinh, Y.-C. J. inorg. Biochem. 42, 87–96 (1991).

    CAS  Article  Google Scholar 

  28. Zumstein, L. & Wang, J. C. J. molec. Biol. 191, 333–340 (1986).

    CAS  Article  Google Scholar 

  29. Lindsay, J. & Wang, J. C. Proc. natn. Acad. Sci. U.S.A. 88, 10485–10489 (1991).

    ADS  Article  Google Scholar 

  30. Roca, J. & Wang, J. C. Cell 71, 833–840 (1992).

    CAS  Article  Google Scholar 

  31. Grau, U. M., Tromer, W. E. & Rossmann, M. G. J. molec. Biol. 151, 289–307 (1981).

    CAS  Article  Google Scholar 

  32. Eklund, H. Samana, J.-P. & Jones, T. A. Biochemistry 23, 5982–5996 (1984).

    CAS  Article  Google Scholar 

  33. Van der Laan, J. M. et al. Biochemistry 28, 7199–7205 (1989).

    CAS  Article  Google Scholar 

  34. Karplus, P. A. & Schulz, G. E. J. molec. Biol. 195, 701–729 (1987).

    CAS  Article  Google Scholar 

  35. Kirkegaard, K., Pflugfelder, G. & Wang, J. C. Cold Spring Harbor Symp. quant. Biol. 49, 411–419 (1984).

    CAS  Article  Google Scholar 

  36. Gilson, M. K., Sharp, K. A. & Honig, B. H. J. comp. Chem. 9, 327–335 (1987).

    Article  Google Scholar 

  37. Nicholls, A., Sharp, K. A. & Honig, B. H. Prot. Struct. Fund. Genet. 11, 281–286 (1991).

    CAS  Article  Google Scholar 

  38. Beran-Steed, R. K. & Tse-Dinh, Y.-C. Prot. Struct. Funct. Genet. 6, 249–258 (1989).

    CAS  Article  Google Scholar 

  39. Kong, X.-P., Onrust, R., O'Donnell, M. & Kuriyan, J. Cell 69, 425–437 (1992).

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  41. Kim, J. L., Nikolov, D. B. & Burley, S. K. Nature 356, 520–527 (1993).

    ADS  Article  Google Scholar 

  42. Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. Nature 365, 512–520 (1993).

    ADS  CAS  Article  Google Scholar 

  43. Brown, P. O. & Cozzarelli, N. R. Proc. natn. Acad. Sci. U.S.A. 78, 843–847 (1981).

    ADS  CAS  Article  Google Scholar 

  44. Tse, Y.-C. & Wang, J. C. Cell 22, 269–277 (1980).

    CAS  Article  Google Scholar 

  45. Kirkegaard, K. & Wang, J. C. J. molec. Biol. 185, 625–637 (1985).

    CAS  Article  Google Scholar 

  46. Champoux, J. J. in DNA Topology and its Biological Effects (eds Cozzarelli, N. R. & Wang, J. C.) 217–242 (Cold Spring Harbor Laboratory Press, New York, 1990).

    Google Scholar 

  47. Durbin, R. M. et al. Science 232, 1127–1132 (1986).

    ADS  CAS  Article  Google Scholar 

  48. Blum, M., Metcalf, P., Harrison, S. C. & Wiley, D. C. J. appl. Cryst. 20, 235–242 (1987).

    CAS  Article  Google Scholar 

  49. Harrison, S. C. J. appl. Cryst. 1, 84–90 (1968).

    Article  Google Scholar 

  50. Kabsch, W. J. appl. Cryst. 21, 67–71 (1988).

    CAS  Article  Google Scholar 

  51. Kabsch, W. J. appl. Cryst. 21, 916–924 (1988).

    CAS  Article  Google Scholar 

  52. Hope, H. Acta. crystallogr. B44, 22–26 (1988).

    CAS  Article  Google Scholar 

  53. CCP4 SERC (UK) Collaborative Computing Project 4 (Daresbury Laboratory, Warrington WA44AD, 1979).

  54. Teng, T.-Y. J. appl. Cryst. 23, 387–391 (1990).

    CAS  Article  Google Scholar 

  55. Otwinowski, Z. in Isomorphous Replacement and Anomalous Scattering 80–86 (Daresbury Laboratory, UK (1991).

    Google Scholar 

  56. Wang, B. C. Meth. Enzym. 115, 90–112 (1985).

    CAS  Article  Google Scholar 

  57. Leslie, A. G. W. Acta. crystallogr. A43, 134–135 (1987).

    Article  Google Scholar 

  58. Sim, G. A. Acta. crystallogr. 13, 511–512 (1960).

    Article  Google Scholar 

  59. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. J. appl. Cryst. 26, 283–291 (1993).

    CAS  Article  Google Scholar 

  60. Kraulis, P. J. J. appl. Cryst. 24, 946–950 (1991).

    Article  Google Scholar 

  61. Evans, S. V. J. molec. Graph. 11, 134–138 (1993).

    CAS  Article  Google Scholar 

  62. Ivey, D. M., Cheng, J. & Krulwich, T. A. Nucleic Acids Res. 20, 4928 (1992).

    CAS  Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois, 60208, USA

    Christopher D. Lima & Alfonso Mondragón

  2. Department of Biochemistry and Molecular Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachussetts, 02138, USA

    James C. Wang & Alfonso Mondragón

Authors
  1. Christopher D. Lima
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. James C. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alfonso Mondragón
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lima, C., Wang, J. & Mondragón, A. Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature 367, 138–146 (1994). https://doi.org/10.1038/367138a0

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/367138a0

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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