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Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase

Nature Structural Biology volume 7, pages 461–465 (2000)Cite this article

Abstract

Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion present in the active site of threonyl-tRNA synthetase, we have determined the crystal structures of complexes of an active truncated form of the enzyme with a threonyl adenylate analog or threonine. The zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl. Amino acid activation experiments reveal that the enzyme shows no activation of isosteric valine, and activates serine at a rate 1,000-fold less than that of cognate threonine. This study demonstrates that the zinc ion is neither strictly catalytic nor structural and suggests how the zinc ion ensures that only amino acids that possess a hydroxyl group attached to the β-position are activated.

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Figure 1: The active site of ΔN-ThrRS with Thr-AMS ligand.
Figure 2: Comparison of threonine, Thr-AMS and Ser-AMS ligands as seen bound to their respective aaRS
Figure 3: Activation experiments with cognate and noncognate amino acids.

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References

  1. Meinnel, T., Mechulam, Y. & Blanquet, S. In Aminoacyl-tRNA synthetase: occurence, structure, and function (Söll, D. & RajBhandary, U.L. eds) 251–291 (ASM Press, Washington DC; 1995).

    Google Scholar 

  2. Fersht, A. Enzyme, structure and mechanism (W. H. Freeman and Company, New York; 1985).

    Google Scholar 

  3. Jakubowski, H. & Goldman, E. Microbiol. Rev. 56, 412–429 (1992).

    Article  CAS  Google Scholar 

  4. Baldwin, A.N. & Berg, P. J. Biol. Chem. 241, 839–845 (1966).

    Article  CAS  Google Scholar 

  5. Loftfield, R.B. & Vanderjagt, M.A. Biochem. J. 128, 1353–1356 (1972).

    Article  CAS  Google Scholar 

  6. Schmidt, E. & Schimmel, P. Science 264, 265–267 (1994).

    Article  CAS  Google Scholar 

  7. Nureki, O. et al. Science 280, 578–582 (1998).

    Article  CAS  Google Scholar 

  8. Fersht, A.R. Science 280, 541 (1998).

    Article  CAS  Google Scholar 

  9. Lin, L., Hale, S.P. & Schimmel, P. Nature 384, 33–34 (1996).

    Article  CAS  Google Scholar 

  10. Silvian, L.F., Wang, J. & Steitz, T.A. Science 285, 1074–1077 (1999).

    Article  CAS  Google Scholar 

  11. Nomanbhoy, T.K., Hendrickson, T.L. & Schimmel, P. Mol. Cell 4, 519–528 (1999).

    Article  CAS  Google Scholar 

  12. Tsui, W.C. & Fersht, A.R. Nucleic Acids Res. 9, 4627–4637 (1981).

    Article  CAS  Google Scholar 

  13. Sankaranarayanan, R. et al. Cell 97, 371–381 (1999).

    Article  CAS  Google Scholar 

  14. Arnez, J.G. & Moras, D. Trends Biochem. Sci. 22, 211–216 (1997).

    Article  CAS  Google Scholar 

  15. Alberts, I.L., Nadassy, K. & Wodak, S.J. Protein Sci. 7, 1700–1716 (1998).

    Article  CAS  Google Scholar 

  16. Cavarelli, J. et al. EMBO J. 13, 327–337 (1994).

    Article  CAS  Google Scholar 

  17. Belrhali, H. et al. Science 263, 1432–1436 (1994).

    Article  CAS  Google Scholar 

  18. Arnez, J.G., Augustine, J.G., Moras, D. & Francklyn, C.S. Proc. Natl. Acad. Sci. 94, 7144–7149 (1997).

    Article  CAS  Google Scholar 

  19. Schmitt, E. et al. EMBO J. 17, 5227–5237 (1998).

    Article  CAS  Google Scholar 

  20. Eigner, E.A. & Loftfield, R.B. Methods Enzymol. 29, 601–619 (1974).

    Article  CAS  Google Scholar 

  21. Igloi, G.L., von der Haar, F. & Cramer, F. Methods Enzymol. 59, 282–291 (1979).

    Article  CAS  Google Scholar 

  22. Fersht, A.R., Shindler, J.S. & Tsui, W.C. Biochemistry 19, 5520–5524 (1980).

    Article  CAS  Google Scholar 

  23. Christner, P., Carpousis, A., Harsch, M. & Rosenbloom, J. J. Biol. Chem. 250, 7623–7630 (1975).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  28. Collaborative Computational Project Number 4. CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

  29. Evans, S.V. J. Mol. Graphics 11, 134–138 (1993).

    Article  CAS  Google Scholar 

  30. Hodel, A., Kim, S.-H. & Brunger, A.T. Acta Crystallogr. A 48, 851–859 (1992).

    Article  Google Scholar 

Download references

Acknowledgements

We thank P. Schimmel for a critical reading of the manuscript. We would like to acknowledge the encouragement and support received from M. Springer, B. Ehresmann and C. Ehresmann. This work was supported by grants from an EEC project, CNRS, INSERM, ULP, and Ministère de la Recherche et de la Technologie.

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Authors and Affiliations

  1. UPR 9004 Biologie Structurale, IGBMC, CNRS/INSERM/ULP, Illkirch Cedex, BP163-67404, France

    Rajan Sankaranarayanan, Anne-Catherine Dock-Bregeon, Bernard Rees & Dino Moras

  2. Department of Biochemistry, College of Medicine, University of Vermont, Burlington, 05405, Vermont, USA

    Michael Bovee & Christopher S. Francklyn

  3. UPR 9073 du CNRS, IBPC, 13 rue P. et M. Curie, 75005, Paris, France

    Joel Caillet

  4. UPR 9002 du CNRS, IBMC, 15 rue Rene Descartes, Strasbourg, 67084, Cedex, France

    Pascale Romby

Authors
  1. Rajan Sankaranarayanan
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  2. Anne-Catherine Dock-Bregeon
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  8. Dino Moras
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Correspondence to Dino Moras.

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Sankaranarayanan, R., Dock-Bregeon, AC., Rees, B. et al. Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nat Struct Mol Biol 7, 461–465 (2000). https://doi.org/10.1038/75856

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