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Crystal structures of restrictocin–inhibitor complexes with implications for RNA recognition and base flipping

Abstract

The cytotoxin sarcin disrupts elongation factor binding and protein synthesis by specifically cleaving one phosphodiester bond in ribosomes. To elucidate the molecular basis of toxin action, we determined three cocrystal structures of the sarcin homolog restrictocin bound to different analogs that mimic the target sarcin/ricin loop (SRL) structure of the rat 28S rRNA. In these structures, restrictocin contacts the bulged-G motif and an unfolded form of the tetraloop of the SRL RNA. In one structure, toxin loops guide selection of the target site by contacting the base critical for recognition (G4319) and the surrounding S-shaped backbone. In another structure, base flipping of the tetraloop enables cleavage by placing the target nucleotide in the active site with the nucleophile nearly inline for attack on the scissile bond. These structures provide the first views of how a site-specific protein endonuclease recognizes and cleaves a folded RNA substrate.

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Figure 1: Structural overview.
Figure 2: Recognition of the identity element, G4319.
Figure 3: Unfolding of the tetraloop enables cleavage.
Figure 4: Implications for cleavage and recognition.

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References

  1. Steyaert, J. Eur. J. Biochem. 247, 1–11 (1997).

    Article  CAS  Google Scholar 

  2. Arni, R.K. et al. Biochemistry 38, 2452–2461 (1999).

    Article  CAS  Google Scholar 

  3. Wool, I.G. In Ribonucleases structures and function (eds D'Alessio, G. & Riordan, J.F.) 131–162 (Academic Press, Inc., San Diego; 1997).

    Book  Google Scholar 

  4. Olmo, N. et al. Eur. J. Biochem. 268, 2113–2123 (2001).

    Article  CAS  Google Scholar 

  5. Yang, X. & Moffat, K. Structure 4, 837–852 (1996).

    Article  CAS  Google Scholar 

  6. Lacadena, J. et al. Proteins 37, 474–484 (1999).

    Article  CAS  Google Scholar 

  7. Kao, R. & Davies, J. J. Biol. Chem. 274, 12576–12582 (1999).

    Article  CAS  Google Scholar 

  8. Munishkin, A. & Wool, I.G. Proc. Natl. Acad. Sci. USA 94, 12280–12284 (1997).

    Article  CAS  Google Scholar 

  9. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. Science 289, 905–920 (2000).

    Article  CAS  Google Scholar 

  10. Moore, P.B. Annu. Rev. Biochem. 68, 287–300 (1999).

    Article  CAS  Google Scholar 

  11. Correll, C.C. et al. Proc. Natl. Acad. Sci. USA 95, 13436–13441 (1998).

    Article  CAS  Google Scholar 

  12. Moazed, D., Robertson, J.M. & Noller, H.F. Nature 334, 362–364 (1988).

    Article  CAS  Google Scholar 

  13. Takeda, E., Bi, X., Yoshinari, S. & Endo, Y. Nucleic Acids Symp. 37, 131–132 (1997).

    CAS  Google Scholar 

  14. Gluck, A., Endo, Y. & Wool, I.G. Nucleic Acids Res. 22, 321–324 (1994).

    Article  CAS  Google Scholar 

  15. Correll, C.C., Wool, I.G. & Munishkin, A. J. Mol. Biol. 292, 275–287 (1999).

    Article  CAS  Google Scholar 

  16. Antao, V.P., Lai, S.Y. & Tinoco, I. Nucleic Acids Res. 19, 5901–5905 (1991).

    Article  CAS  Google Scholar 

  17. Endo, Y., Gluck, A., Chan, Y.L., Tsurugi, K. & Wool, I.G. J. Biol. Chem. 265, 2216–2222 (1990).

    CAS  PubMed  Google Scholar 

  18. Soukup, G.A. & Breaker, R.R. RNA 5, 1308–1325 (1999).

    Article  CAS  Google Scholar 

  19. Diener, J.L. & Moore, P.B. Mol. Cell 1, 883–894 (1998).

    Article  CAS  Google Scholar 

  20. Scott, W.G., Finch, J.T. & Klug, A. Cell 81, 991–1002 (1995).

    Article  CAS  Google Scholar 

  21. Cai, Z. & Tinoco, I. Biochemistry 35, 6026–6036 (1996).

    Article  CAS  Google Scholar 

  22. Wedekind, J.E. & McKay, D.B. Nature Struct. Biol. 6, 261–268 (1999).

    Article  CAS  Google Scholar 

  23. Rupert, P.B. & Ferre-D'Amare, A.R. Nature 410, 780–786 (2001).

    Article  CAS  Google Scholar 

  24. Richards, F.M. et al. Cold Spring Harbor Symp. Quant. Biol. 36, 35–43 (1971).

    Article  CAS  Google Scholar 

  25. Li, H., Trotta, C.R. & Abelson, J. Science 280, 279–284 (1998).

    Article  CAS  Google Scholar 

  26. Weston, S.A., Tucker, A.D., Thatcher, D.R., Derbyshire, D.J. & Pauptit, R.A. J. Mol. Biol. 244, 410–422 (1994).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  28. Roberts, R.J. & Cheng, X. Annu. Rev. Biochem. 67, 181–198 (1998).

    Article  CAS  Google Scholar 

  29. Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  30. Navaza, J. Acta Crystallogr. A 50, 157–163 (1994).

    Article  Google Scholar 

  31. Read, R.J. Acta Crstallolgr. A 42, 140–149 (1986).

    Article  Google Scholar 

  32. Cowtan, K.D. & Zhang, K.Y. Prog. Biophys. Mol. Biol. 72, 245–270 (1999).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  35. Carson, M. Methods Enzymol. 277, 493–505 (1991).

    Article  Google Scholar 

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

    Article  Google Scholar 

  37. Seggerson, K. & Moore, P.B. RNA 4, 1203–1215 (1998).

    Article  CAS  Google Scholar 

  38. Wimberly, B.T., Guymon, R., McCutcheon, J.P., White, S.W. & Ramakrishnan, V. Cell 97, 491–502. (1999).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. Beneken, Y. Chen, A. Glück, T. Pan, P. Rice and I. Wool for helpful discussion and the staff of BioCARS for help with data collection. A Cancer Research Foundation Young Investigator Award and grant from the NIH to C.C.C. supported this work.

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Correspondence to Carl C. Correll.

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Yang, X., Gérczei, T., Glover, L. et al. Crystal structures of restrictocin–inhibitor complexes with implications for RNA recognition and base flipping. Nat Struct Mol Biol 8, 968–973 (2001). https://doi.org/10.1038/nsb1101-968

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