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

Author

Listed:
  • Niels Fischer

    (Max Planck Institute for Biophysical Chemistry)

  • Piotr Neumann

    (Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen)

  • Lars V. Bock

    (Max Planck Institute for Biophysical Chemistry)

  • Cristina Maracci

    (Max Planck Institute for Biophysical Chemistry)

  • Zhe Wang

    (Institute of Complex Systems (ICS-6))

  • Alena Paleskava

    (Max Planck Institute for Biophysical Chemistry
    †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.).)

  • Andrey L. Konevega

    (Max Planck Institute for Biophysical Chemistry
    †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.).)

  • Gunnar F Schröder

    (Institute of Complex Systems (ICS-6)
    Heinrich-Heine Universität Düsseldorf)

  • Helmut Grubmüller

    (Max Planck Institute for Biophysical Chemistry)

  • Ralf Ficner

    (Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen)

  • Marina V. Rodnina

    (Max Planck Institute for Biophysical Chemistry)

  • Holger Stark

    (Max Planck Institute for Biophysical Chemistry)

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.

Suggested Citation

  • Niels Fischer & Piotr Neumann & Lars V. Bock & Cristina Maracci & Zhe Wang & Alena Paleskava & Andrey L. Konevega & Gunnar F Schröder & Helmut Grubmüller & Ralf Ficner & Marina V. Rodnina & Holger Sta, 2016. "The pathway to GTPase activation of elongation factor SelB on the ribosome," Nature, Nature, vol. 540(7631), pages 80-85, December.
    • Handle: RePEc:nat:nature:v:540:y:2016:i:7631:d:10.1038_nature20560
    DOI: 10.1038/nature20560
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    Cited by:

    1. Sakshi Jain & Lukasz Koziej & Panagiotis Poulis & Igor Kaczmarczyk & Monika Gaik & Michal Rawski & Namit Ranjan & Sebastian Glatt & Marina V. Rodnina, 2023. "Modulation of translational decoding by m6A modification of mRNA," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Valentyn Petrychenko & Bee-Zen Peng & Ana C. A. P. Schwarzer & Frank Peske & Marina V. Rodnina & Niels Fischer, 2021. "Structural mechanism of GTPase-powered ribosome-tRNA movement," Nature Communications, Nature, vol. 12(1), pages 1-9, December.

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