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A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution

Nature Structural Biology volume 6, pages 318–321 (1999)Cite this article

Abstract

The Tetrahymena ribozyme is a metalloenzyme that catalyzes cleavage of oligonucleotide substrates by phosphoryl transfer. Thiophilic metal ions such as Mn2+, Zn2+ or Cd2+ rescue the >103-fold inhibitory effect of sulfur substitution of the 3'-oxygen leaving group but do not effectively rescue the effect of sulfur substitution of the nonbridging pro-Sp phosphoryl oxygen. We now show that the latter effect can be fully rescued by Zn2+ or Cd2+ using a phosphorodithioate substrate, in which both the 3'-oxygen and the pro-Sp oxygen are simultaneously substituted with sulfur. These results provide the first functional evidence that metallophosphotransferases can mediate catalysis via metal ion coordination to both the leaving group and a nonbridging oxygen of the scissile phosphate.

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Figure 1: a, Schematic diagram of the Tetrahymena ribozyme cleavage reaction.
Figure 2: Mn2+ partially rescues the deleterious effect of sulfur substitution of the pro-Sp oxygen.
Figure 3: Metal ion specificity switch in the endonuclease reaction of a Sp phosphorodithioate substrate.
Figure 4: A new metal ion interaction in the Tetrahymena ribozyme reaction.

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References

  1. Zaug, A.J., Been, M.D. & Cech, T.R. Nature 324, 429– 433 (1986).

    Article  CAS  Google Scholar 

  2. Zaug, A.J., Grosshans, C.A. & Cech, T.R. Biochemistry 27, 8924– 8931 (1988).

    Article  CAS  Google Scholar 

  3. Herschlag, D. & Cech, T.R. Biochemistry 29, 10172–10180 (1990).

    Article  CAS  Google Scholar 

  4. Robertson, D.L. & Joyce, G.F. Nature 344, 467–468 (1990).

    Article  CAS  Google Scholar 

  5. Kruger, K. et al. Cell 31, 147–157 (1982).

    Article  CAS  Google Scholar 

  6. Cech, T.R. & Herschlag, D. Nucleic Acids Mol. Biol. 10, 1–17 (1996).

    Article  CAS  Google Scholar 

  7. Herschlag, D. & Cech, T.R. Biochemistry 29, 10159–10171 (1990).

    Article  CAS  Google Scholar 

  8. Piccirilli, J.A., Vyle, J.S., Caruthers, M.H. & Cech, T.R. Nature 361, 85–88 ( 1993).

    Article  CAS  Google Scholar 

  9. Jaffe, E.K. & Cohn, M. J. Biol. Chem. 253, 4823–4825 (1978).

    CAS  PubMed  Google Scholar 

  10. Pecoraro, V.L., Hermes, J.D. & Cleland, W.W. Biochemistry 23, 5262– 5271 (1984).

    Article  CAS  Google Scholar 

  11. Sigel, R.K.O., Song, B. & Sigel, H. J. Am. Chem. Soc. 119, 744–755 (1997).

    Article  CAS  Google Scholar 

  12. Weinstein, L.B., Jones, B.C., Cosstick, R. & Cech, T.R. Nature 388, 805–808 ( 1997).

    Article  CAS  Google Scholar 

  13. Herschlag, D., Piccirilli, J.A. & Cech, T.R. Biochemistry 30, 4844– 4854 (1991).

    Article  CAS  Google Scholar 

  14. McConnell, T.S. & Cech, T.R. Biochemistry 34, 4056–4067 (1995).

    Article  CAS  Google Scholar 

  15. Cosstick, R. & Vyle, J.S. Nucleic Acids Res. 18 , 829–835 (1990).

    Article  CAS  Google Scholar 

  16. Rudinger, J. et al. Proc. Natl. Acad. Sci. USA 89, 5882 –5886 (1992).

    Article  CAS  Google Scholar 

  17. McSwiggen, J.A. & Cech, T.R. Science 244, 679–683 (1989).

    Article  CAS  Google Scholar 

  18. Rajagopal, J., Doudna, J.A. & Szostak, J.W. Science 244, 692– 694 (1989).

    Article  CAS  Google Scholar 

  19. Hansma, H.G., Laney, D.E. Biophys. J. 70, 1933–1939 (1996).

    Article  CAS  Google Scholar 

  20. Pan, T., Long, D.M. & Uhlenbeck, O.C. in The RNA World (eds. Gesteland, R.F. & Atkins, J.F.) 271–302 (Cold Spring Harbor Laboratory Press, Plainview, New York, 1993).

    Google Scholar 

  21. Weinstein, L.B., Earnshaw, D.J., Cosstick, R. & Cech, T.R. J. Am. Chem. Soc. 118, 10341–10350 (1996).

    Article  CAS  Google Scholar 

  22. Frey, P.A. & Sammons, R.D. Science 228, 541–545 (1985).

    Article  CAS  Google Scholar 

  23. Wang, P. et al. J. Am. Chem. Soc. 113, 55– 64 (1991).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  25. Steitz, T.A. Curr. Opin. Struct. Biol. 3, 31–38 (1993).

    Article  CAS  Google Scholar 

  26. Kim, E.E. & Wyckoff, H.W. J. Mol. Biol. 218, 449–464 (1991).

    Article  CAS  Google Scholar 

  27. Steitz, T.A. & Steitz, J.A. Proc Natl. Acad. Sci USA 90, 6498–6502 (1993).

    Article  CAS  Google Scholar 

  28. Curely, J.F., Joyce, C.M. & Piccirilli, J.A. J. Am. Chem. Soc. 119, 12691 –12692 (1997).

    Article  Google Scholar 

  29. Sontheimer, E.J., Sun, S. & Piccirilli, J.A. Nature 388, 801– 805 (1997).

    Article  CAS  Google Scholar 

  30. Koizumi, M. & Ohtsuka, E. Biochemistry 30, 5145–5150 (1991).

    Article  CAS  Google Scholar 

  31. Slim, G. & Gait, M.J. Nucleic Acids Res. 19 , 1183–1188 (1991).

    Article  CAS  Google Scholar 

  32. Warnecke, J.M., Furste, J.P., Hardt, W.D., Erdmann, V.A. & Hartmann, R.K. Proc Natl. Acad. Sci. USA 93, 8924–8928 (1996).

    Article  CAS  Google Scholar 

  33. Sun, S., Yoshida, A. & Piccirilli, J.A. RNA 3, 1352– 1363 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Knitt, D.S., Narlikar, G.J. & Herschlag, D. Biochemistry 33, 13864– 13879 (1994).

    Article  CAS  Google Scholar 

  35. Herschlag, D. Biochemistry 31, 1386–1399 (1992).

    Article  CAS  Google Scholar 

  36. Diakun, G.P., Fairall, L. & Klug, A. Nature 324, 698– 699 (1986).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank D. Herschlag and S. Shan for critical evaluation of the manuscript and for helpful discussions throughout the course of this work. We also thank J. Curley, P. Gordon, M. Hamm, E. Sontheimer, and the referees for critical comments on the manuscript. J.A.P. is an assistant investigator of the Howard Hughes Medical Institute.

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Author notes

  1. Sengen Sun

    Present address: The R. W. Johnson Pharmaceutical Research Institute, 1000 Route 202, Raritan, New Jersey, 08869, USA

Authors and Affiliations

  1. Departments of Biochemistry and Molecular Biology, and Chemistry, Howard Hughes Medical Institute, The University of Chicago, 5841 S. Maryland Ave., MC 1028, Chicago, 60637, Illinois, USA

    Aiichiro Yoshida, Sengen Sun & Joseph A. Piccirilli

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  1. Aiichiro Yoshida
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  2. Sengen Sun
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  3. Joseph A. Piccirilli
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Correspondence to Joseph A. Piccirilli.

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Yoshida, A., Sun, S. & Piccirilli, J. A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nat Struct Mol Biol 6, 318–321 (1999). https://doi.org/10.1038/7551

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