A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome

Nat Struct Mol Biol. 2014 Sep;21(9):787-93. doi: 10.1038/nsmb.2871. Epub 2014 Aug 17.


During peptide-bond formation on the ribosome, the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-Å resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.

Publication types

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

MeSH terms

  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Models, Molecular
  • Peptides / chemistry
  • Peptides / metabolism*
  • Protons
  • RNA, Transfer, Amino Acyl / chemistry
  • RNA, Transfer, Amino Acyl / metabolism*
  • Ribosomes / chemistry
  • Ribosomes / metabolism*
  • Thermus thermophilus / chemistry
  • Thermus thermophilus / metabolism*
  • Water / metabolism


  • Peptides
  • Protons
  • RNA, Transfer, Amino Acyl
  • Water

Associated data

  • PDB/4QCM
  • PDB/4QCN
  • PDB/4QCO
  • PDB/4QCP
  • PDB/4QCQ
  • PDB/4QCR
  • PDB/4QCS
  • PDB/4QCT
  • PDB/4QCU
  • PDB/4QCV
  • PDB/4QCW
  • PDB/4QCX
  • PDB/4QCY
  • PDB/4QCZ
  • PDB/4QD0
  • PDB/4QD1