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.

Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB

Nature volume 424, pages 699–703 (2003)Cite this article

Abstract

Accurate translation of genetic information into protein sequence depends on complete messenger RNA molecules. Truncated mRNAs cause synthesis of defective proteins, and arrest ribosomes at the end of their incomplete message. In bacteria, a hybrid RNA molecule that combines the functions of both transfer and messenger RNAs (called tmRNA) rescues stalled ribosomes, and targets aberrant, partially synthesized, proteins for proteolytic degradation1,2. Here we report the 3.2-Å-resolution structure of the tRNA-like domain of tmRNA (tmRNAΔ) in complex with small protein B (SmpB), a protein essential for biological functions of tmRNA. We find that the flexible RNA molecule adopts an open L-shaped conformation and SmpB binds to its elbow region, stabilizing the single-stranded D-loop in an extended conformation. The most striking feature of the structure of tmRNAΔ is a 90° rotation of the TΨC-arm around the helical axis. Owing to this unusual conformation, the SmpB–tmRNAΔ complex positioned into the A-site of the ribosome orients SmpB towards the small ribosomal subunit, and directs tmRNA towards the elongation-factor binding region of the ribosome. On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

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

Figure 1: Overview of the SmpB–tmRNAΔ structure.
Figure 2: Two views of tmRNAΔ in comparison with tRNAPhe (ref. 14).
Figure 3: SmpB–tmRNAΔ interactions.
Figure 4: Model of the interactions between the SmpB–tmRNAΔ complex and the ribosome.

References

  1. Karzai, A. W., Roche, E. D. & Sauer, R. T. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nature Struct. Biol. 7, 449–455 (2000)

    Article  CAS  Google Scholar 

  2. Keiler, K. C., Waller, P. R. & Sauer, R. T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993 (1996)

    Article  ADS  CAS  Google Scholar 

  3. Karzai, A. W., Susskind, M. M. & Sauer, R. T. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 18, 3793–3799 (1999)

    Article  CAS  Google Scholar 

  4. Rudinger-Thirion, J., Giege, R. & Felden, B. Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. RNA 5, 989–992 (1999)

    Article  CAS  Google Scholar 

  5. Gottesman, S., Roche, E., Zhou, Y. & Sauer, R. T. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338–1347 (1998)

    Article  CAS  Google Scholar 

  6. Keiler, K. C., Shapiro, L. & Williams, K. P. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc. Natl Acad. Sci. USA 97, 7778–7783 (2000)

    Article  ADS  CAS  Google Scholar 

  7. Williams, K. P. & Bartel, D. P. Phylogenetic analysis of tmRNA secondary structure. RNA 2, 1306–1310 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Felden, B. et al. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). RNA 3, 89–103 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Someya, T. et al. Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus. FEBS Lett. 535, 94–100 (2003)

    Article  CAS  Google Scholar 

  10. Dong, G., Nowakowski, J. & Hoffman, D. W. Structure of small protein B: The protein component of the tmRNA-SmpB system for ribosome rescue. EMBO J. 21, 1845–1854 (2002)

    Article  CAS  Google Scholar 

  11. Kim, S. H. Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain. Science 179, 285–288 (1973)

    Article  ADS  CAS  Google Scholar 

  12. Ushida, C., Himeno, H., Watanabe, T. & Muto, A. tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis. Nucleic Acids Res. 22, 3392–3396 (1994)

    Article  CAS  Google Scholar 

  13. Komine, Y., Kitabatake, M. & Inokuchi, H. 10Sa RNA.is associated with 70S ribosome particles in Escherichia coli. J. Biochem. (Tokyo) 119, 463–467 (1996)

    Article  CAS  Google Scholar 

  14. Shi, H. & Moore, P. B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited. RNA 6, 1091–1105 (2000)

    Article  CAS  Google Scholar 

  15. Stagg, S. M., Frazer-Abel, A. A., Hagerman, P. J. & Harvey, S. C. Structural studies of the tRNA domain of tmRNA. J. Mol. Biol. 309, 727–735 (2001)

    Article  CAS  Google Scholar 

  16. Hanawa-Suetsugu, K., Bordeau, V., Himeno, H., Muto, A. & Felden, B. Importance of the conserved nucleotides around the tRNA-like structure of Escherichia coli transfer-messenger RNA for protein tagging. Nucleic Acids Res. 29, 4663–4673 (2001)

    Article  CAS  Google Scholar 

  17. Ibba, M. & Soll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69, 617–650 (2000)

    Article  CAS  Google Scholar 

  18. Hou, Y. M. & Schimmel, P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333, 140–145 (1988)

    Article  ADS  CAS  Google Scholar 

  19. McClain, W. H., Foss, K., Jenkins, R. A. & Schneider, J. Four sites in the acceptor helix and one site in the variable pocket of tRNA(Ala) determine the molecule's acceptor identity. Proc. Natl Acad. Sci. USA 88, 9272–9276 (1991)

    Article  ADS  CAS  Google Scholar 

  20. Barends, S., Karzai, A. W., Sauer, R. T., Wower, J. & Kraal, B. Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA. J. Mol. Biol. 314, 9–21 (2001)

    Article  CAS  Google Scholar 

  21. Valle, M. et al. Visualizing tmRNA entry into a stalled ribosome. Science 300, 127–130 (2003)

    Article  ADS  CAS  Google Scholar 

  22. Price, S. R., Ito, N., Oubridge, C., Avis, J. M. & Nagai, K. Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J. Mol. Biol. 249, 398–408 (1995)

    Article  CAS  Google Scholar 

  23. Corvaisier, S., Bordeau, V. & Felden, B. Inhibition of transfer messenger RNA aminoacylation and trans-translation by aminoglycoside antibiotics. J. Biol. Chem. 278, 14788–14797 (2003)

    Article  CAS  Google Scholar 

  24. Otwinowski, Z. & Minor, W. Processing X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  25. Terwilliger, T. C. Automated structure solution, density modification and model building. Acta Crystallogr. D 58, 1937–1940 (2002)

    Article  Google Scholar 

  26. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D. 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  27. Jones, T. A., Zou, 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 

  28. DeLano, W. L. The PyMOL Molecular Graphics System 〈http://www.pymol.org〉 (2002).

  29. Ban, N., Nissen, P., Hansen, J., 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  CAS  Google Scholar 

  30. 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 

Download references

Acknowledgements

We thank C. Schulze-Briese, T. Tomizaki and A. Wagner (SLS, Villigen) D. Sargent, and the team at Swiss Norwegian Beamline (ESRF, Grenoble) for assistance in data collection, V. Ramakrishnan for comments on the manuscript, and D. Goven for help in the footprint assays. P.W.H. is supported by an EMBO fellowship. This work was supported by the Swiss National Science Foundation (SNSF), the NCCR Structural Biology programme of the SNSF, and a Young Investigator grant from the Human Frontier Science Program.

Author information

Authors and Affiliations

  1. Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg (ETH Zürich), HPK Gebäude, CH-8093, Zürich, Switzerland

    Sascha Gutmann, Peter W. Haebel, Markus Sutter & Nenad Ban

  2. Biochimie Pharmaceutique UPRES JE2311, Université de Rennes I, avenue du Pr. Léon Bernard, CS 34317, F-35043 Cedex, Rennes, France

    Laurent Metzinger & Brice Felden

Authors
  1. Sascha Gutmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter W. Haebel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Laurent Metzinger
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Markus Sutter
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Brice Felden
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nenad Ban
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nenad Ban.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

41586_2003_BFnature01831_MOESM1_ESM.jpg

Supplementary Figure 1: Chemical and enzymatic footprints of tmRNAΔ as free molecule and in complex with SmpB. (JPG 135 kb)

Supplementary Figure Legend (DOC 20 kb)

Supplementary Table 1: containing data collection, phasing and refinement statistics. (DOC 26 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Gutmann, S., Haebel, P., Metzinger, L. et al. Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature 424, 699–703 (2003). https://doi.org/10.1038/nature01831

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature01831

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