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Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I

Nature Structural Biology volume 8, pages 62–67 (2001)Cite this article

Abstract

We have solved the crystal structure of the Holliday junction resolving enzyme T7 endonuclease I at 2.1 Å resolution using the multiwavelength anomalous dispersion (MAD) technique. Endonuclease I exhibits strong structural specificity for four-way DNA junctions. The structure shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site. While no significant structural similarity could be detected with any other junction resolving enzyme, the active site is similar to that found in several restriction endonucleases. T7 endonuclease I therefore represents the first crystal structure of a junction resolving enzyme that is a member of the nuclease superfamily of enzymes.

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Figure 1: Amino acid sequence of T7 endonuclease I expressed in E. coli and stereo views showing representative portions of the final refined, 2Fo − Fc electron density maps at 2.1 Å.
Figure 2: Structure and active site of endonuclease I.
Figure 3: Comparison of the active site of endonuclease I with restriction endonucleases.
Figure 4: Comparison of the structures of a, T7 endonuclease I, b, T4 endonuclease VII (PDB entry 1EN7) and c, RuvC (PDB entry 1HJR) viewed along their two-fold symmetry axes.

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References

  1. Holliday, R. Genet. Res, 5, 282–304 (1964).

    Article  Google Scholar 

  2. Orr-Weaver, T.L., Szostak, J.W. & Rothstein, R.J. Proc. Natl. Acad. Sci. USA 78, 6354–6358 (1981).

    Article  CAS  Google Scholar 

  3. Potter, H. & Dressler, D. Proc. Natl. Acad. Sci. USA 73, 3000–3004 (1976).

    Article  CAS  Google Scholar 

  4. Schwacha, A. & Kleckner, N. Cell 83, 783–791 (1995).

    Article  CAS  Google Scholar 

  5. Duckett, D.R., Giraud-Panis, M.-J.E. & Lilley, D.M.J. J. Mol. Biol. 246, 95–107 (1995).

    Article  CAS  Google Scholar 

  6. Pöhler, J.R.G., Giraud-Panis, M.-J.E. & Lilley, D.M.J. J. Mol. Biol. 260, 678–696 (1996).

    Article  Google Scholar 

  7. White, M.F. & Lilley, D.M.J. J. Mol. Biol. 257, 330–341 (1996).

    Article  CAS  Google Scholar 

  8. Studier, F.W. Virology 39, 562–574 (1969).

    Article  CAS  Google Scholar 

  9. de Massey, B., Studier, F.W., Dorgai, L., Appelbaum, F. & Weisberg, R.A. Cold Spring Harbor Symp. Quant. Biol. 49, 715–726 (1984).

    Article  Google Scholar 

  10. de Massey, B., Weisberg, R.A. & Studier, F.W. J. Mol. Biol. 193, 359–376 (1987).

    Article  Google Scholar 

  11. Dickie, P., McFadden, G. & Morgan, A.R. J. Biol. Chem. 262, 14826–14836 (1987).

    CAS  PubMed  Google Scholar 

  12. Kerr, C. & Sadowski, P.D. Virology 65, 281–285 (1975).

    Article  CAS  Google Scholar 

  13. Powling, A. & Knippers, R. Mol. Gen. Genet. 149, 63–71 (1976).

    Article  CAS  Google Scholar 

  14. Tsujimoto, Y. & Ogawa, H. J. Mol. Biol. 125, 255–273 (1978).

    Article  CAS  Google Scholar 

  15. Parkinson, M.J. & Lilley, D.M.J. J. Mol. Biol. 270, 169–178 (1997).

    Article  CAS  Google Scholar 

  16. Ariyoshi, M. et al. Cell 78, 1063–1072 (1994).

    Article  CAS  Google Scholar 

  17. Raaijmakers, H. et al. EMBO J. 18, 1447–1458 (1999).

    Article  CAS  Google Scholar 

  18. Terwilliger, T.C. & Berendzen, J. Acta Crystallogr. D 53, 571–579 (1997).

    Article  CAS  Google Scholar 

  19. Collaborative Computational Project, Number 4. Acta Crystallogr. D 50, 760–763 (1994).

  20. Rafferty, J.B. et al. Science 274, 415–421 (1996).

    Article  CAS  Google Scholar 

  21. Guo, F., Gopaul, D.N. & Van Duyne, G.D. Nature 389, 40–46 (1997).

    Article  CAS  Google Scholar 

  22. Parkinson, M J., Pöhler, J.R.G. & Lilley, D.M.J. Nucleic Acids Res. 27, 682–689 (1999).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  25. Kim, Y., Grable, J.C., Love, R., Greene, P.J. & Rosenberg, J.M. Science 249, 1307–1309 (1990).

    Article  CAS  Google Scholar 

  26. Wah, D.A., Hirsch, J.A., Dorner, L.F., Schildkraut, I. & Aggarwal, A.K. Nature 388, 97–100 (1997).

    Article  CAS  Google Scholar 

  27. Pingould, A. & Jeltsch, A. Eur. J. Biochem. 246, 1–22 (1997).

    Article  Google Scholar 

  28. Lee, J., Jayaram, M. & Grainge, I. EMBO J. 18, 784–791 (1999).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  31. Bozic, D., Grazulis, S., Siksnys, V. & Huber, R. J. Mol. Biol. 255, 176–186 (1996).

    Article  CAS  Google Scholar 

  32. Hickman, A.B. et al. Mol. Cell. 5, 1025–1034 (2000).

    Article  CAS  Google Scholar 

  33. Hargreaves, D. et al. Nature Struct. Biol. 5, 441–445 (1998).

    Article  CAS  Google Scholar 

  34. Eichman, B.F., Vargason, J.M., Mooers, B.H.M. & Ho, P.S. Proc. Natl. Acad. Sci. USA 97, 3971–3976 (2000).

    Article  CAS  Google Scholar 

  35. Giraud-Panis, M.-J.E. & Lilley, D.M.J. J. Biol. Chem. 271, 33148–33155 (1996).

    Article  CAS  Google Scholar 

  36. Kvaratskhelia, M., Wardleworth, B.N., Norman, D.G. & White, M.F. J. Biol. Chem. 275, 25540–25546 (2000).

    Article  CAS  Google Scholar 

  37. Ban, C. & Yang, W. EMBO J. 17, 1526–1534 (1998).

    Article  CAS  Google Scholar 

  38. Kovall, R. & Matthews, B.W. Science 277, 1824–1827 (1997).

    Article  CAS  Google Scholar 

  39. Lilley, D.M.J. & White, M.F. Proc. Natl. Acad. Sci. USA 97, 9351–9353 (2000).

    Article  CAS  Google Scholar 

  40. LeMaster, D.M. & Richards, F.M. Biochemistry 24, 7263–7268 (1985).

    Article  CAS  Google Scholar 

  41. Graber, P. et al. Eur. J. Biochem. 212, 751–755 (1993).

    Article  CAS  Google Scholar 

  42. Leslie, A.G.W. MOSFLM. (MRC Laboratory of Molecular Biology, Cambridge, UK; 1996).

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

    Article  Google Scholar 

  44. Brünger, A.T. X-PLOR 3.1: a system for crystallography and NMR (Yale University Press, New Haven, Conneticut; 1993).

    Google Scholar 

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

    Article  Google Scholar 

  46. Duckett, D.R. et al. Cell 55, 79–89 (1988).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  48. Christopher, J.A. The Spock Homepage: http://quorum.tamu.edu/spock/ (1998).

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Acknowledgements

We would like to thank G. Leonard, S. Azrt, R. Ravelli, and S. McSweeney for help with data collection at the European Synchrotron Radiation Facility and the staff of the Daresbury SRS for assistance with preliminary studies. We are grateful to the Wellcome Trust and the Cancer Research Campaign for financial support and for facilities provided by the BBSRC-funded North of England Structural Biology Centre (NESBIC).

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  1. Máire A. Convery

    Present address: Molecular Recognition Department, Glaxo Wellcome Research and Development, Gunnels Wood Road, Stevenage, Hertfordshire, UK

Authors and Affiliations

  1. Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK

    Jonathan M. Hadden, Máire A. Convery & Simon E.V. Phillips

  2. Department of Biochemistry, CRC Nucleic Acid Structure Research Group, University of Dundee, Dundee, DD1 4HN, UK

    Anne-Cécile Déclais & David M.J. Lilley

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Correspondence to Simon E.V. Phillips.

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Hadden, J., Convery, M., Déclais, AC. et al. Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I. Nat Struct Mol Biol 8, 62–67 (2001). https://doi.org/10.1038/83067

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