The location and the significance of a cross-link between the sarcin/ricin domain of ribosomal RNA and the elongation factor-G

J Mol Biol. 2004 Mar 19;337(2):263-72. doi: 10.1016/j.jmb.2004.01.020.

Abstract

During translocation peptidyl-tRNA moves from the A-site to the P-site and mRNA is displaced by three nucleotides in the 3' direction. This reaction is catalyzed by elongation factor-G (EF-G) and is associated with ribosome-dependent hydrolysis of GTP. The molecular basis of translocation is the most important unsolved problem with respect to ribosome function. A critical question, one that might provide a clue to the mechanism of translocation, is the precise identity of the contacts between EF-G and ribosome components. To make the identification, a covalent bond was formed, by ultraviolet irradiation, between EF-G and a sarcin/ricin domain (SRD) oligoribonucleotide containing 5-iodouridine. The cross-link was established, by mass spectroscopy and by Edman degradation, to be between a tryptophan at position 127 in the G domain in EF-G and either one of two 5-iodouridine nucleotides in the sequence UAG2655U in the SRD. G2655 is a critical identity element for the recognition of the factor's ribosomal binding site. The site of the cross-link provides the first direct evidence that the SRD is in close proximity to the EF-G catalytic center. The proximity suggests that the SRD RNA has a role in the activation of GTP hydrolysis that leads to a transition in the conformation of the factor and to its release from the ribosome.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites / genetics
  • Cross-Linking Reagents
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Elongation Factor G / chemistry*
  • Peptide Elongation Factor G / metabolism*
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Ribosomal / chemistry*
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / metabolism*
  • Ricin / chemistry*
  • Ricin / metabolism*
  • Sequence Homology, Amino Acid
  • Thermus thermophilus / genetics
  • Thermus thermophilus / metabolism
  • Ultraviolet Rays

Substances

  • Bacterial Proteins
  • Cross-Linking Reagents
  • Escherichia coli Proteins
  • Macromolecular Substances
  • Peptide Elongation Factor G
  • RNA, Bacterial
  • RNA, Ribosomal
  • Ricin