Elongation factor 4 remodels the A-site tRNA on the ribosome

Proc Natl Acad Sci U S A. 2016 May 3;113(18):4994-9. doi: 10.1073/pnas.1522932113. Epub 2016 Apr 18.

Abstract

During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. The structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.

Keywords: elongation factor 4; protein–RNA interactions; remodeling; ribosome; tRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / ultrastructure*
  • Molecular Docking Simulation
  • Nucleic Acid Conformation
  • Peptide Initiation Factors / chemistry*
  • Peptide Initiation Factors / ultrastructure*
  • Protein Binding
  • Protein Conformation
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / ultrastructure*
  • RNA, Transfer / chemistry*
  • RNA, Transfer / ultrastructure*
  • RNA-Binding Motifs
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / ultrastructure
  • Ribosomes

Substances

  • Escherichia coli Proteins
  • LepA protein, E coli
  • Peptide Initiation Factors
  • RNA, Bacterial
  • RNA-Binding Proteins
  • RNA, Transfer

Associated data

  • PDB/5J8B