Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome

Science. 2009 Aug 21;325(5943):966-70. doi: 10.1126/science.1175800.

Abstract

Elongation factor P (EF-P) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. Here we report the crystal structure of EF-P bound to the Thermus thermophilus 70S ribosome along with the initiator transfer RNA N-formyl-methionyl-tRNA(i) (fMet-tRNA(i)(fMet)) and a short piece of messenger RNA (mRNA) at a resolution of 3.5 angstroms. EF-P binds to a site located between the binding site for the peptidyl tRNA (P site) and the exiting tRNA (E site). It spans both ribosomal subunits with its amino-terminal domain positioned adjacent to the aminoacyl acceptor stem and its carboxyl-terminal domain positioned next to the anticodon stem-loop of the P site-bound initiator tRNA. Domain II of EF-P interacts with the ribosomal protein L1, which results in the largest movement of the L1 stalk that has been observed in the absence of ratcheting of the ribosomal subunits. EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • Models, Molecular
  • Peptide Chain Initiation, Translational*
  • Peptide Elongation Factors / chemistry*
  • Peptide Elongation Factors / metabolism*
  • Protein Conformation
  • Protein Structure, Tertiary
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism
  • RNA, Transfer, Met / chemistry
  • RNA, Transfer, Met / metabolism
  • Ribosomal Proteins / metabolism
  • Ribosome Subunits, Large, Bacterial / metabolism
  • Ribosome Subunits, Small, Bacterial / metabolism
  • Ribosomes / metabolism*
  • Thermus thermophilus / chemistry
  • Thermus thermophilus / metabolism*

Substances

  • Bacterial Proteins
  • Peptide Elongation Factors
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Transfer, Met
  • Ribosomal Proteins
  • fMet-tRNA(fMet)
  • factor EF-P
  • ribosomal protein L1

Associated data

  • PDB/3HUW
  • PDB/3HUX
  • PDB/3HUY
  • PDB/3HUZ