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A cryo-electron microscopic study of ribosome-bound termination factor RF2

Nature volume 421, pages 87–90 (2003)Cite this article

Abstract

Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit1,2. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit3. The distance between the DC and PTC is ∼73 Å. However, in the X-ray structure of RF2, SPF and GGQ are only 23 Å apart4, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF–stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.

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Figure 1: Interaction of RC with RF2.
Figure 2: CPK (Corey–Pauling–Koltun) representation of RF2 domain constellations in the two conformations.
Figure 3: Stereo views showing interaction between functional centres on the RC and RF2 domains.

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References

  1. Kisselev, L. L. & Buckingham, R. H. Translational termination comes of age. Trends Biochem. Sci. 25, 561–566 (2000)

    Article  CAS  Google Scholar 

  2. Zavialov, A. V., Mora, L., Buckingham, R. M. & Ehrenberg, M. Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol. Cell 10, 789–798 (2002)

    Article  CAS  Google Scholar 

  3. Ito, K., Ebihara, K. & Nakamura, Y. A tripeptide anticodon deciphers stop codons in messenger RNA. Nature 403, 680–684 (2000)

    Article  ADS  CAS  Google Scholar 

  4. Vestergaard, B. et al. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol. Cell 8, 1375–1382 (2001)

    Article  CAS  Google Scholar 

  5. Zavialov, A. V., Buckingham, R. H. & Ehrenberg, M. A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107, 115–124 (2001)

    Article  CAS  Google Scholar 

  6. Wimberly, B. T., Guymon, R., McCutcheon, J. P., White, S. W. & Ramakrishnan, V. R. A detailed view of the ribosomal active site: the structure of the L11–RNA complex. Cell 97, 491–502 (1999)

    Article  CAS  Google Scholar 

  7. Gerstein, M., Lesk, A. M. & Chothia, C. Structural mechanisms for domain movements in proteins. Biochemistry 33, 6739–6749 (1994)

    Article  CAS  Google Scholar 

  8. Ramakrishnan, V. Ribosome structure and the mechanism of translation. Cell 108, 557–572 (2002)

    Article  CAS  Google Scholar 

  9. Tate, W. P., Dognin, M. J., Noah, M., Stöffler-Meilicke, M. & Stöffler, G. The NH2 terminal domain of Escherichia coli ribosomal protein L11. J. Biol. Chem. 259, 7317–7324 (1984)

    CAS  PubMed  Google Scholar 

  10. Brot, N., Tate, W. P., Caskey, C. T. & Weissbach, H. Requirement for ribosomal proteins L7 and L12 in peptide-chain termination. Proc. Natl Acad. Sci. USA 71, 89–92 (1974)

    Article  ADS  CAS  Google Scholar 

  11. Arkov, A. L. & Murgola, E. J. Ribosomal RNAs in translation termination: facts and hypothesis. Biochemistry (Moscow) 64, 1354–1359 (1999)

    CAS  Google Scholar 

  12. Seit-Nebi, A., Frolova, L., Justesen, J. & Kisselev, L. Class-1 translation termination factors: invariant GGQ minidomain is essential for release activity and ribosomal binding but not for stop codon recognition. Nucleic Acids Res. 29, 3982–3987 (2001)

    Article  CAS  Google Scholar 

  13. Song, H. et al. The crystal structure of human eukaryotic release factor eRF1—mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 100, 311–321 (2000)

    Article  CAS  Google Scholar 

  14. Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000)

    Article  ADS  CAS  Google Scholar 

  15. Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 4, 897–902 (2001)

    Google Scholar 

  16. Drugeon, G. et al. Eukaryotic release factor 1 (eRF1) abolishes readthrough and competes with suppressor tRNAs at all the three termination codons in messenger RNA. Nucleic Acids Res. 25, 2254–2258 (1997)

    Article  CAS  Google Scholar 

  17. Tate, W. P., Greuer, B. & Brimacombe, R. Codon recognition in polypeptide chain termination: site directed cross linking of termination codon to Escherichia coli release factor 2. Nucleic Acids Res. 18, 6537–6544 (1990)

    Article  CAS  Google Scholar 

  18. Wilson, K. S., Ito, K., Noller, H. F. & Nakamura, Y. Functional sites of interaction between release factor RF1 and the ribosome. Nature Struct. Biol. 7, 866–870 (2000)

    Article  CAS  Google Scholar 

  19. Ito, K., Ebihara, K., Uno, M. & Nakamura, Y. Conserved motifs in prokaryotic and eukaryotic polypeptide release factors: tRNA-protein mimicry hypothesis. Proc. Natl Acad. Sci. USA 93, 5443–5448 (1996)

    Article  ADS  CAS  Google Scholar 

  20. Jelenc, P. C. & Kurland, C. G. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl Acad. Sci. USA 76, 3174–3178 (1979)

    Article  ADS  CAS  Google Scholar 

  21. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996)

    Article  CAS  Google Scholar 

  22. Orlova, E. V. et al. Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution. J. Mol. Biol. 271, 417–437 (1997)

    Article  CAS  Google Scholar 

  23. Gabashvili, I. S. et al. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100, 537–549 (2000)

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  25. Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000)

    Article  ADS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  27. Yusupova, G. Z., Yusupov, M. M., Cate, J. H. & Noller, H. F. The path of messenger RNA through the ribosome. Cell 106, 233–241 (2001)

    Article  CAS  Google Scholar 

  28. Carson, M. Ribbons 2.0. J. Appl. Cryst. 24, 103–106 (1991)

    Article  Google Scholar 

Download references

Acknowledgements

We thank M. Kjeldgaard (University of Aarhaus, Denmark) for pre-releasing the RF2 coordinates, T. Tenson (Tarfu University, Estonia) for a critical reading of the manuscript and helpful suggestions, and M. Watters for assistance with the illustrations. This work was supported by the Howard Hughes Medical Institute and by grants from the National Institute of Health (to J.F.) and by the Swedish Foundation for Strategic Research and the Swedish Research Council (to A.V.Z. and M.E.).

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Author notes

  1. Urmila B. S. Rawat, Andrey V. Zavialov and Joachim Frank: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Health Research, Inc., Empire State Plaza, Albany, NY, 12201-0509, USA

    Urmila B. S. Rawat, Mikel Valle, Robert A. Grassucci & Joachim Frank

  2. Wadsworth Center, Empire State Plaza, Albany, New York, 12201-0509, USA

    Urmila B. S. Rawat, Jayati Sengupta, Mikel Valle, Robert A. Grassucci, Jamie Linde & Joachim Frank

  3. Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, 5-75124, Uppsala, Sweden

    Andrey V. Zavialov & Måns Ehrenberg

  4. Institute of Molecular and Structural Biology, University of Aarhus, DK-8000 C, Aarhus, Denmark

    Bente Vestergaard

  5. Department of Biomedical Sciences, State University of New York at Albany, New York, 12222, USA

    Joachim Frank

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Correspondence to Joachim Frank.

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Rawat, U., Zavialov, A., Sengupta, J. et al. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421, 87–90 (2003). https://doi.org/10.1038/nature01224

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