title: The pathway to GTPase activation of elongation factor SelB on the ribosome.
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-tRNASecrecodes 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-tRNASecbinding by SelB and show large-scale rearrangements of Sec-tRNASec. Upon initial binding of SelB-Sec-tRNASecto the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNASeccovering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNASecaway 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.
authors.affiliation: Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Niels
authors.initials: N
authors.lastname: Fischer
authors.affiliation: Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany.
authors.forename: Piotr
authors.initials: P
authors.lastname: Neumann
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Lars V
authors.initials: LV
authors.lastname: Bock
authors.affiliation: Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Cristina
authors.initials: C
authors.lastname: Maracci
authors.affiliation: Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Alena
authors.initials: A
authors.lastname: Paleskava
authors.affiliation: Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Andrey L
authors.initials: AL
authors.lastname: Konevega
authors.affiliation: Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.|Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Gunnar F
authors.initials: GF
authors.lastname: Schröder
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Helmut
authors.initials: H
authors.lastname: Grubmüller
authors.affiliation: Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Ficner
authors.affiliation: Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
authors.affiliation: Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Stark
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure; D001665:Binding Sites; D018388:Codon, Terminator / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020285:Cryoelectron Microscopy; D004722:Endoribonucleases / Q000378:metabolism; D004789:Enzyme Activation; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D005656:Fungal Proteins / Q000378:metabolism; D020558:GTP Phosphohydrolases / Q000378:metabolism* / Q000648:ultrastructure; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D014176:Protein Biosynthesis; D000072417:Protein Domains; D012345:RNA, Transfer, Amino Acid-Specific / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D054681:Ribosome Subunits, Large, Bacterial / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D012270:Ribosomes / Q000737:chemistry / Q000201:enzymology / Q000378:metabolism* / Q000648:ultrastructure; D012276:Ricin / Q000378:metabolism; D017279:Selenocysteine / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D018388:Codon, Terminator; D005656:Fungal Proteins; D012345:RNA, Transfer, Amino Acid-Specific; C061878:SelB protein, Bacteria; C036928:tRNA, selenocysteine-; D017279:Selenocysteine; C014801:alpha-sarcin; D012276:Ricin; D004722:Endoribonucleases; D020558:GTP Phosphohydrolases