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The pathway to GTPase activation of elongation factor SelB on the ribosome

Nature volume 540, pages 8085 (01 December 2016) | Download Citation

Abstract

In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNASec) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNASec recodes a UGA stop codon next to a downstream mRNA stem–loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNASec binding by SelB and show large-scale rearrangements of Sec-tRNASec. Upon initial binding of SelB–Sec-tRNASec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNASec covering the sarcin–ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNASec away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.

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Acknowledgements

We thank F. Würriehausen, A. Bursy, O. Geintzer, S. Kappler, C. Kothe, T. Niese, T. Wiles, and M. Zimmermann for expert technical assistance and M. Lüttich and T. Koske for support in high-performance computation. The work was supported by the Deutsche Forschungsgemeinschaft Grant FOR 1805 (to H.S., M.V.R. and H.G.) and by the Sonderforschungsbereich 860 (to R.F.).

Author information

Author notes

    • Alena Paleskava
    •  & Andrey L. Konevega

    Present addresses: Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute of National Research Centre ‘Kurchatov Institute’, 188300 Gatchina, Russia (A.P., A.L.K.); St Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St Petersburg, Russia (A.P., A.L.K.).

Affiliations

  1. Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany

    • Niels Fischer
    •  & Holger Stark
  2. Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany

    • Piotr Neumann
    •  & Ralf Ficner
  3. Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany

    • Lars V. Bock
    •  & Helmut Grubmüller
  4. Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany

    • Cristina Maracci
    • , Alena Paleskava
    • , Andrey L. Konevega
    •  & Marina V. Rodnina
  5. Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany

    • Zhe Wang
    •  & Gunnar F Schröder
  6. Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany

    • Gunnar F Schröder

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Contributions

N.F. conceived the project, performed cryo-EM experiments and data analysis and drafted the paper. P.N. built atomic models and performed pseudo-crystallographic refinement. L.V.B. performed and analyzed molecular dynamics simulations. C.M. performed the kinetic analysis. A.P. and A.L.K prepared ribosome complexes for cryo-EM. Z.W. and G.F.S. performed homology modelling. N.F., M.V.R. and H.S. finalized the paper with inputs from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Niels Fischer or Holger Stark.

Reviewer Information Nature thanks A. Amunts, M. Wahl and S. Yokoyama for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature20560

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