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

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 Stark

doi:10.1038/nature20560

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

Nature. 2016 Dec 1;540(7631):80-85. doi: 10.1038/nature20560. Epub 2016 Nov 14.

Authors

Affiliations

¹ Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
² Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany.
³ Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
⁴ Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
⁵ Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
⁶ Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany.

PMID: 27842381
DOI: 10.1038/nature20560

Abstract

In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA^Sec) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA^Sec 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-tRNA^Sec binding by SelB and show large-scale rearrangements of Sec-tRNA^Sec. Upon initial binding of SelB-Sec-tRNA^Sec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA^Sec 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-tRNA^Sec 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / chemistry
Bacterial Proteins / metabolism*
Bacterial Proteins / ultrastructure
Binding Sites
Codon, Terminator / chemistry
Codon, Terminator / genetics
Codon, Terminator / metabolism
Cryoelectron Microscopy
Endoribonucleases / metabolism
Enzyme Activation
Escherichia coli / chemistry
Escherichia coli / genetics
Escherichia coli / metabolism*
Escherichia coli / ultrastructure
Fungal Proteins / metabolism
GTP Phosphohydrolases / metabolism*
GTP Phosphohydrolases / ultrastructure
Models, Molecular
Nucleic Acid Conformation
Protein Binding
Protein Biosynthesis
Protein Domains
RNA, Transfer, Amino Acid-Specific / chemistry
RNA, Transfer, Amino Acid-Specific / genetics
RNA, Transfer, Amino Acid-Specific / metabolism
RNA, Transfer, Amino Acid-Specific / ultrastructure
Ribosome Subunits, Large, Bacterial / chemistry
Ribosome Subunits, Large, Bacterial / metabolism
Ribosome Subunits, Large, Bacterial / ultrastructure
Ribosome Subunits, Small, Bacterial / chemistry
Ribosome Subunits, Small, Bacterial / metabolism
Ribosome Subunits, Small, Bacterial / ultrastructure
Ribosomes / chemistry
Ribosomes / enzymology
Ribosomes / metabolism*
Ribosomes / ultrastructure
Ricin / metabolism
Selenocysteine / metabolism

Substances

Bacterial Proteins
Codon, Terminator
Fungal Proteins
RNA, Transfer, Amino Acid-Specific
SelB protein, Bacteria
tRNA, selenocysteine-
Selenocysteine
alpha-sarcin
Ricin
Endoribonucleases
GTP Phosphohydrolases