Interaction between the two conserved single-stranded regions at the decoding site of small subunit ribosomal RNA is essential for ribosome function

Biochemistry. 1992 Dec 8;31(48):12012-22. doi: 10.1021/bi00163a008.


Formation of the tertiary base pair G1401:C1501, which brings together two universally present and highly sequence-conserved single-stranded segments of small subunit ribosomal RNA, is essential for ribosome function. It was previously reported that mutation of G1401 inactivated all in vitro functions of the ribosome [Cunningham et al. (1992) Biochemistry 31, 7629-7637]. Here we show that mutation of C1501 to G was equally inactivating but that the double mutant C1401:G1501 with the base pair reversed had virtually full activity for tRNA binding to the P, A, and I sites and for peptide bond formation. Initiation-dependent formation of the first peptide bond remained 70-85% inhibited, despite full 70S initiation complex formation ability as evidenced by the ability to form fMET-puromycin. These results suggest that the defect in formation of the first peptide bond lies in filling the initial A site, Ai, rather than the subsequent elongation A sites, Ae. An increased mobility around the anticodon was detected by UV cross-linking of the anticodon of P-site-bound tRNA to C1399 as well as to the expected C1400. These findings provide the first experimental evidence for the existence of the G1401:C1501 base pair and show that this base pair, located at the decoding site, is essential for function. The structural implications of tertiary base pair formation are discussed.

MeSH terms

  • Base Sequence
  • Binding Sites
  • Cross-Linking Reagents
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Molecular Sequence Data
  • Mutation
  • N-Formylmethionine / metabolism
  • Nucleic Acid Conformation
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / metabolism*
  • RNA, Transfer / metabolism
  • Ribosomes / metabolism*
  • Transcription, Genetic


  • Cross-Linking Reagents
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • N-Formylmethionine
  • RNA, Transfer