The identification of the determinants of the cyclic, sequential binding of elongation factors tu and g to the ribosome

J Mol Biol. 2009 Feb 27;386(3):802-13. doi: 10.1016/j.jmb.2008.12.071. Epub 2009 Jan 6.

Abstract

Experiments dedicated to gaining an understanding of the mechanism underlying the orderly, sequential association of elongation factor Tu (EF-Tu) and elongation factor G (EF-G) with the ribosome during protein synthesis were undertaken. The binding of one EF is always followed by the binding of the other, despite the two sharing the same-or a largely overlapping-site and despite the two having isosteric structures. Aminoacyl-tRNA, peptidyl-tRNA, and deacylated-tRNA were bound in various combinations to the A-site, P-site, or E-site of ribosomes, and their effect on conformation in the peptidyl transferase center, the GTPase-associated center, and the sarcin/ricin domain (SRD) was determined. In addition, the effect of the ribosome complexes on sensitivity to the ribotoxins sarcin and pokeweed antiviral protein and on the binding of EF-G*GTP were assessed. The results support the following conclusions: the EF-Tu ternary complex binds to the A-site whenever it is vacant and the P-site has peptidyl-tRNA; and association of the EF-Tu ternary complex is prevented, simply by steric hindrance, when the A-site is occupied by peptidyl-tRNA. On the other hand, the affinity of the ribosome for EF-G*GTP is increased when peptidyl-tRNA is in the A-site, and the increase is the result of a conformational change in the SRD. We propose that peptidyl-tRNA in the A-site is an effector that initiates a series of changes in tertiary interactions between nucleotides in the peptidyl transferase center, the SRD, and the GTPase-associated center of 23S rRNA; and that the signal, transmitted through a transduction pathway, informs the ribosome of the position of peptidyl-tRNA and leads to a conformational change in the SRD that favors binding of EF-G.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Binding Sites
  • Escherichia coli / chemistry
  • Escherichia coli / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Elongation Factor G / metabolism*
  • Peptide Elongation Factor Tu / metabolism*
  • Protein Binding
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism
  • RNA, Ribosomal, 23S / chemistry
  • RNA, Ribosomal, 23S / metabolism
  • Ribosome Subunits, Large, Bacterial / chemistry
  • Ribosomes / chemistry*
  • Ribosomes / metabolism*

Substances

  • Peptide Elongation Factor G
  • RNA, Bacterial
  • RNA, Ribosomal, 23S
  • Peptide Elongation Factor Tu