Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Hypothesis
  • Published:

The transorientation hypothesis for codon recognition during protein synthesis

Nature volume 416, pages 281–285 (2002)Cite this article

Abstract

During decoding, a codon of messenger RNA is matched with its cognate aminoacyl-transfer RNA and the amino acid carried by the tRNA is added to the growing protein chain. Here we propose a molecular mechanism for the decoding phase of translation: the transorientation hypothesis. The model incorporates a newly identified tRNA binding site and utilizes a flip between two tRNA anticodon loop structures, the 5′-stacked and the 3′-stacked conformations. The anticodon loop acts as a three-dimensional hinge permitting rotation of the tRNA about a relatively fixed codon–anticodon pair. This rotation, driven by a conformational change in elongation factor Tu involving GTP hydrolysis, transorients the incoming tRNA into the A site from the D site of initial binding and decoding, where it can be proofread and accommodated. The proposed mechanisms are compatible with the known structures, conformations and functions of the ribosome and its component parts including tRNAs and EF-Tu, in both the GTP and GDP states.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The structures of tRNAs and their orientation on the 30S subunit.
Figure 2: The ternary complex docked into the 70S D site.
Figure 3: The ternary complex docked in the D site, illustrating steric clash with the 50S L11–RNA complex.
Figure 4: Schematic representation of the ribosome, mRNA and tRNAs during decoding.

Similar content being viewed by others

References

  1. Garrett, R. A. et al. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions (ASM, Washington DC, 2000).

    Google Scholar 

  2. Pape, T., Wintermeyer, W. & Rodnina, M. V. Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 17, 7490–7497 (1998).

    Article  CAS  Google Scholar 

  3. Hopfield, J. J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl Acad. Sci. USA 71, 4135–4139 (1974).

    Article  ADS  CAS  Google Scholar 

  4. Nierhaus, K. H. The allosteric three-site model for the ribosomal elongation cycle: features and future. Biochemistry 29, 4997–5008 (1990).

    Article  CAS  Google Scholar 

  5. Agrawal, R. K. et al. Direct visualization of A-, P-, and E-site transfer RNAs in the E. coli ribosome. Science 271, 1000–1002 (1996).

    Article  ADS  CAS  Google Scholar 

  6. Wimberly, B. T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000).

    Article  ADS  CAS  Google Scholar 

  7. Carter, A. P. et al. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407, 340–348 (2000).

    Article  ADS  CAS  Google Scholar 

  8. Stark, H. et al. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389, 403–406 (1997).

    Article  ADS  CAS  Google Scholar 

  9. Agrawal, R. K., Penczek, P., Grassucci, R. A. & Frank, J. Visualization of elongation factor G on the Escherichia coli ribosome: the mechanism of translocation. Proc. Natl Acad. Sci. USA 95, 6134–6138 (1998).

    Article  ADS  CAS  Google Scholar 

  10. Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896 (2001).

    Article  ADS  CAS  Google Scholar 

  11. Ban, N. et al. the complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000).

    Article  ADS  CAS  Google Scholar 

  12. Schluenzen, F. et al. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102, 615–623 (2000).

    Article  CAS  Google Scholar 

  13. Nissen, P. et al. Crystal structure of the ternary complex of the Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270, 1464–1472 (1995).

    Article  ADS  CAS  Google Scholar 

  14. Lake, J. A. Aminoacyl-tRNA binding at the recognition site is the first step of the elongation cycle of protein synthesis. Proc. Natl Acad. Sci. USA 74, 1903–1907 (1977).

    Article  ADS  CAS  Google Scholar 

  15. Fuller, W. & Hodgson, A. Conformation of the anticodon loop in tRNA. Nature 215, 817–821 (1967).

    Article  ADS  CAS  Google Scholar 

  16. Woese, C. Molecular mechanics of translation: a reciprocating ratchet mechanism. Nature 226, 817–820 (1970).

    Article  ADS  CAS  Google Scholar 

  17. Crick, F. H. C., Brenner, S., Klug, A. & Pieczenik, G. Speculation on the origin of protein synthesis. Orig. Life 7, 389–397 (1976).

    Article  ADS  CAS  Google Scholar 

  18. Ladner, J. E. et al. Structure of yeast phenylalanine transfer RNA at 2.5 Å resolution. Proc. Natl Acad. Sci. USA 72, 4414–4418 (1975).

    Article  ADS  CAS  Google Scholar 

  19. Quigley, G. J., Seeman, N. C., Wang, A., Suddath, F. L. & Rich, A. Yeast phenylalanine transfer RNA: Atomic coordinates and torsion angles. Nucleic Acids Res. 2, 2329–2349 (1975).

    Article  CAS  Google Scholar 

  20. Eiler, S. et al. Synthesis of aspartyl-tRNAAsp in Escherichia coli—a snapshot of the second step. EMBO J. 18, 6532–6541 (1999).

    Article  CAS  Google Scholar 

  21. Gupta, S. L., Waterson, J., Sopori, M. L., Weissman, S. M. & Lengyel, P. Movement of the ribosome along the messenger ribonucleic acid during protein synthesis. Biochemistry 10, 4410–4421 (1971).

    Article  CAS  Google Scholar 

  22. Thach, S. S. & Thach, R. E. Translocation of messenger RNA and accommodation of fMet-tRNA. Proc. Natl Acad. Sci. USA 68, 1791–1795 (1971).

    Article  ADS  CAS  Google Scholar 

  23. Harada, F. & Dahlberg, J. E. Specific cleavage of tRNA by nuclease S1. Nucleic Acids Res. 2, 865–871 (1975).

    Article  CAS  Google Scholar 

  24. Tal, J. The cleavage of transfer RNA by a single strand specific endonuclease from Neurospora crassa. Nucleic Acids Res. 2, 1073–1082 (1975).

    Article  CAS  Google Scholar 

  25. Wrede, P., Woo, N. H. & Rich, A. Initiator tRNAs have a unique anticodon loop conformation. Proc. Natl Acad. Sci. USA 76, 3289–3293 (1979).

    Article  ADS  CAS  Google Scholar 

  26. Schweisguth, D. C. & Moore, P. B. On the conformation of the anticodon loops of initiator and elongator methionine tRNAs. J. Mol. Biol. 267, 505–519 (1997).

    Article  CAS  Google Scholar 

  27. Klug, A. et al. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. Mol. Biol. 131, 669–680 (1979).

    Article  CAS  Google Scholar 

  28. Dickerson, R. E. & Chiu, T. K. Helix bending as a factor in protein/DNA recognition. Biopolymers 44, 361–403 (1997).

    Article  CAS  Google Scholar 

  29. Carbon, J. & Fleck, E. W. Genetic alteration of structure and function in glycine transfer RNA of Escherichia coli: mechanism of suppression of the tryptophan synthetase A78 mutation. J. Mol. Biol. 85, 371–391 (1974).

    Article  CAS  Google Scholar 

  30. Gefter, M. L. & Russell, R. L. Role modifications in tyrosine transfer RNA: a modified base affecting ribosome binding. J. Mol. Biol. 39, 145–157 (1969).

    Article  CAS  Google Scholar 

  31. Strycharz, W. A., Nomura, M. & Lake, J. A. Ribosomal proteins L7/L12 localized at a single region of the large subunit by immune electron microscopy. J. Mol. Biol. 126, 123–140 (1978).

    Article  CAS  Google Scholar 

  32. Briones, E., Briones, C., Remacha, M. & Ballesta, J. P. The GTPase center protein L12 is required for correct ribosomal stalk assembly but not for Saccharomyces cerevisiae viability. J. Biol. Chem. 273, 31956–31961 (1998).

    Article  CAS  Google Scholar 

  33. Cundliffe, E. in Structure, Function and Genetics of Ribosomes (eds Hardesty, B. & Kramer, G.) 586–604 (Springer, New York, 1986).

    Book  Google Scholar 

  34. Wimberly, B. T. et al. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Cell 97, 491–502 (1999).

    Article  CAS  Google Scholar 

  35. Markus, M. A. et al. High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA. Nature Struct. Biol. 4, 70–77 (1997).

    Article  CAS  Google Scholar 

  36. Stoeffler, G., Cundliffe, E., Stoeffler-Meilicke, M. & Dabbs, E. R. Mutants of Escherichia coli lacking ribosomal protein L11. J. Biol. Chem. 255, 10517–10522 (1980).

    CAS  Google Scholar 

  37. Polekhina, G. et al. Helix unwinding in the effector region of elongation factor EF-Tu GDP. Structure 4, 1141–1151 (1996).

    Article  CAS  Google Scholar 

  38. Abel, K. et al. An α to β conformational switch in EF-Tu. Structure 4, 1153–1159 (1996).

    Article  CAS  Google Scholar 

  39. Song, H. et al. Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 Å resolution. J. Mol. Biol. 285, 1245–1256 (1999).

    Article  CAS  Google Scholar 

  40. Abdulkarim, F., Liljas, L. & Hughes, D. Mutations to kirromycin resistance occur in the interface of domains I and III of EF-Tu·GTP. FEBS Lett. 352, 118–122 (1994).

    Article  CAS  Google Scholar 

  41. Vogeley, L., Palm, G. J., Mesters, J. R. & Hilgenfeld, R. Conformational change of elongation factor Tu induced by antibiotic binding: crystal structure of the complex between EF-Tu:GDP and aurodox. J. Biol. Chem. 276, 17149–17155 (2001)

    Article  CAS  Google Scholar 

  42. Kurland, C. G. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26, 29–50 (1992).

    Article  CAS  Google Scholar 

  43. Noller, H. F., Hoffarth, V. & Zimniak, L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416–1419 (1992).

    Article  ADS  CAS  Google Scholar 

  44. Zaug, A. J. & Cech, T. R. The intervening sequence RNA of Tetrahymena is an enzyme. Science 231, 470–475 (1986).

    Article  ADS  CAS  Google Scholar 

  45. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

Download references

Acknowledgements

We thank D. Eisenberg and R. Dickerson for advice and for access to graphics terminals and software, A. Maris and D. Cascio for help, M. Rivera, R. Jain and J. Moore for advice, and M. Kowalczyk for the art work. This work was supported by grants to J.A.L. from the National Institutes of Health, the Astrobiology Institute, the National Science Foundation, and the Department of Energy.

Author information

Authors and Affiliations

  1. Molecular Biology Institute, Human Genetics, and MCD Biology, University of California, Los Angeles, 90095, California, USA

    Anne B. Simonson & James A. Lake

Authors
  1. Anne B. Simonson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. James A. Lake
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Anne B. Simonson or James A. Lake.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Simonson, A., Lake, J. The transorientation hypothesis for codon recognition during protein synthesis. Nature 416, 281–285 (2002). https://doi.org/10.1038/416281a

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/416281a

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing