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

• Published in: Nature (London) Vol. 540; no. 7631; pp. 80 - 85
• Main Authors: Fischer, Niels, Neumann, Piotr, Bock, Lars V, Maracci, Cristina, Wang, Zhe, Paleskava, Alena, Konevega, Andrey L, Schröder, Gunnar F, Grubmüller, Helmut, Ficner, Ralf, Rodnina, Marina V, Stark, Holger
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01.12.2016
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bacterial Proteins - ultrastructure; Binding Sites; Codon, Terminator - chemistry; Codon, Terminator - genetics; Codon, Terminator - metabolism; Cryoelectron Microscopy; Crystal structure; E coli; Endoribonucleases - metabolism; Enzyme Activation; Enzymes; Escherichia coli - chemistry; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli - ultrastructure; Fungal Proteins - metabolism; GTP Phosphohydrolases - metabolism; GTP Phosphohydrolases - ultrastructure; Guanosine triphosphatase; Models, Molecular; Nucleic Acid Conformation; Physiological aspects; Protein Binding; Protein Biosynthesis; Protein Domains; Protein research; Ribonucleic acid; 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; Ribosomes - chemistry; Ribosomes - enzymology; Ribosomes - metabolism; Ribosomes - ultrastructure; Ricin - metabolism; RNA; RNA, Transfer, Amino Acid-Specific - chemistry; RNA, Transfer, Amino Acid-Specific - genetics; RNA, Transfer, Amino Acid-Specific - metabolism; RNA, Transfer, Amino Acid-Specific - ultrastructure; Selenocysteine - metabolism
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature20560

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