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Site-specific DNA binding using a variation of the double stranded RNA binding motif

Nature Structural Biology volume 5, pages 546–550 (1998)Cite this article

Abstract

The integrase family of site-specific recombinases catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria and yeast. The solution structure of the DNA binding domain of the integrase protein from the conjugative transposon Tn 916 has been determined using NMR spectroscopy. The structure provides the first insights into distal site DNA binding by a site-specific integrase and reveals that the N-terminal domain is structurally similar to the double stranded RNA binding domain (dsRBD). The results of chemical shift mapping experiments suggest that the integrase protein interacts with DNA using residues located on the face of its three stranded β-sheet. This surface differs from the proposed RNA binding surface in dsRBDs, suggesting that different surfaces on the same protein fold can be used to bind DNA and RNA.

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Figure 1: The Tn916 transposon.
Figure 2: Superposition of 25 simulated annealing structures of the IntN domain (residues Arg 6–Asp 70).
Figure 3: Chemical shift differences between free and DNA bound forms of the IntN domain.
Figure 4: Comparison of the structures of a, IntN domain (residues Arg 6–Asp 70 ) and b, staufen dsRBD III protein22.

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References

  1. Scott, J.R. & Churchward, G. Annu. Rev. Microbiol. 49, 367–397 (1995).

    Article  CAS  Google Scholar 

  2. Clewell, D.B. & Flannagan, S.E. In Bacterial conjugation (ed. Clewell, D.B.) 369–393 (Plenum, New York; 1993).

    Book  Google Scholar 

  3. Clewell, D.B. Flannagan, S.E. & Jaworski, D.D. Trends Microbiol. 3, 229 –236 (1995).

    Article  CAS  Google Scholar 

  4. Argos, P. et al. EMBO J. 5, 433–440 ( 1996).

    Article  Google Scholar 

  5. Glasgow, A.C. Hughes, K.T. & Simon, M.L. In Mobile DNA (eds Berg, D.E. &Howe, M.M.) 637–659 (American Society of Microbiology, Washington DC; 1989).

    Google Scholar 

  6. Blakely, G. et al. Cell 75, 351–361 ( 1993).

    Article  CAS  Google Scholar 

  7. Hoess, R.H. & Abremski, K. In Nucleic Acids and Molecular Biology (eds Eckstein, F. & Lilley, D.M.J.) 99– 109 (Springer-Verlag, Berlin; 1990).

    Book  Google Scholar 

  8. Cox, M.M. In Mobile DNA (eds Berg, D.E. & Howe, M.M.) 661–670 (American Society of Microbiology, Washington DC; 1989).

    Google Scholar 

  9. Golden, J.W. Robinson, S.L. & Haselkorn, R. Nature 314, 419– 423 (1985).

    Article  CAS  Google Scholar 

  10. Stragier, P. Kunkel, B. Kroos, L. & Losick, R. Science 243, 507–512 (1989).

    Article  CAS  Google Scholar 

  11. Thompson, J.F. & Landy, A. In Mobile DNA (eds Berg, D.E. & Howe, M.M.) 1–22 (American Society of Microbiology, Washington DC; 1989).

    Google Scholar 

  12. Lu, F. & Churchward, G. EMBO J. 13, 1541–1548 (1994).

    Article  CAS  Google Scholar 

  13. Landy, A. Ann. Rev. Biochem. 58, 913–949 ( 1989).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  15. Hickman, A.B. Waninger, S. Scocca, J.J. & Dyda, F. Cell 89, 227–237 (1997).

    Article  CAS  Google Scholar 

  16. Kwon, H.J. Tirumalai, R. Landy, A. & Ellenberger, T. Science 276 (1997).

  17. Subramanya, H.S. et al. EMBO J. 16, 5178–5187 (1997).

    Article  CAS  Google Scholar 

  18. Wilmot, C.M. & Thornton, J.M. J. Mol. Biol. 203, 221–232 (1988).

    Article  CAS  Google Scholar 

  19. Presta, L.G. & Rose, G.D. Science 240, 1632–1641 (1988).

    Article  CAS  Google Scholar 

  20. Ramakrishnan, V. & White, S.W. Nature 358, 768–771 (1992).

    Article  CAS  Google Scholar 

  21. Burd, C.G. & Dreyfuss, G. Science 265, 615–620 (1994).

    Article  CAS  Google Scholar 

  22. Bycroft, M. Grunert, S. Murzin, A.G. Proctor, M. & St. Johnson, D. EMBO J. 14,3563– 3571 (1995).

    Article  CAS  Google Scholar 

  23. Kharrat, A. Macias, M.J. Gibson, T.J. Nilges, M. & Pastore, A. EMBO J. 14, 3572– 3584 (1995).

    Article  CAS  Google Scholar 

  24. Ferrandon, D. Elphick, L. Nüsslein-Volhard, C. & St. Johnson, D. Cell 79, 1221–1231 ( 1994).

    Article  CAS  Google Scholar 

  25. Bax, A. & Grzesiek, S. Acct. Chem. Res. 26, 131–138 (1993).

    Article  CAS  Google Scholar 

  26. Clore, G.M. & Gronenborn, A.M. Science 252, 1390–1399 (1991).

    Article  CAS  Google Scholar 

  27. Clore, G.M. & Gronenborn, A.M. (eds) NMR of proteins (CRC Press, Ann Arbor, Michigan; 1993).

    Book  Google Scholar 

  28. Bax, A. et al. Meth. Enzs. 239, 79–106 (1994).

    Article  CAS  Google Scholar 

  29. Delaglio, F. J. Biomolec. NMR 6, 277–293 ( 1995).

    Article  CAS  Google Scholar 

  30. Garrett, D.S. Powers, R. Gronenborn, A.M. & Clore, G.M. J. Magn. Reson. 95, 214–220 ( 1991).

    CAS  Google Scholar 

  31. Nilges, M. Prot. Struct. Funct. Genet. 17, 295–309 (1993).

    Article  Google Scholar 

  32. Ponder, J.W. & Richards, F.M. J. Mol. Biol. 193, 775–791 (1987).

    Article  CAS  Google Scholar 

  33. Brünger, A.T. X-PLOR Manual, Version 3.1. (Yale University, New Haven, Connecticut; 1993).

    Google Scholar 

  34. Garrett, D.S. J. Magn. Reson. Series B 104, 99–103 (1994).

    Article  CAS  Google Scholar 

  35. Kuszewski, J. Qin, J., Gronenborn, A.M. & Clore, G.M. J. Magn. Reson. Series B 106, 92–96 (1996).

    Article  Google Scholar 

  36. Kuszewski, J. Gronenborn, A.M. & Clore, G.M. Prot. Sci. 5, 1067– 1080 (1996).

    Article  CAS  Google Scholar 

  37. Nilges, M. Clore, G.M. & Gronenborn, A.M. FEBS Lett. 229, 129– 136 (1988).

    Article  Google Scholar 

  38. Koradi, R. Billeter, M. & Wuthrich, K. J. Mol. Graphics 14, 51–55 (1996).

    Article  CAS  Google Scholar 

  39. Kraulis, P.J. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

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Acknowledgements

We thank T. Dieckmann and M. Grzeskowiak for technical support; D. Garrett for the program PIPP and F. Delaglio for the program NMRPipe, J. Omichinski for useful discussions and G. Churchward for the Tn916 integrase clone. This work was supported by a grant from the U.S. Department of Energy.

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  1. Department of Chemistry and Biochemistry and UCLA-DOE Laboratory of Structural Biology and Genetics, University of California, Los Angeles, 405 Hilgard Ave, Los Angeles, 90095, California, USA

    Kevin M. Connolly, Jonathan M. Wojciak & Robert T. Clubb

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  1. Kevin M. Connolly
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Correspondence to Robert T. Clubb.

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Connolly, K., Wojciak, J. & Clubb, R. Site-specific DNA binding using a variation of the double stranded RNA binding motif. Nat Struct Mol Biol 5, 546–550 (1998). https://doi.org/10.1038/799

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