The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis

Chem Biol. 2008 May;15(5):485-92. doi: 10.1016/j.chembiol.2008.03.014. Epub 2008 Apr 24.

Abstract

Peptide bond formation is a fundamental reaction in biology, catalyzed by the ribosomal peptidyl-transferase ribozyme. Although all active-site 23S ribosomal RNA nucleotides are universally conserved, atomic mutagenesis suggests that these nucleobases do not carry functional groups directly involved in peptide bond formation. Instead, a single ribose 2'-hydroxyl group at A2451 was identified to be of pivotal importance. Here, we altered the chemical characteristics by replacing its 2'-hydroxyl with selected functional groups and demonstrate that hydrogen donor capability is essential for transpeptidation. We propose that the A2451-2'-hydroxyl directly hydrogen bonds to the P-site tRNA-A76 ribose. This promotes an effective A76 ribose C2'-endo conformation to support amide synthesis via a proton shuttle mechanism. Simultaneously, the direct interaction of A2451 with A76 renders the intramolecular transesterification of the peptide from the 3'- to 2'-oxygen unfeasible, thus promoting effective peptide bond synthesis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Molecular Sequence Data
  • Mutagenesis
  • Nucleic Acid Conformation
  • Peptides / chemical synthesis*
  • RNA, Ribosomal, 23S / chemistry
  • RNA, Ribosomal, 23S / genetics
  • RNA, Ribosomal, 23S / metabolism*

Substances

  • Peptides
  • RNA, Ribosomal, 23S