molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition

Mol Cell. 2005 Jul 22;19(2):235-46. doi: 10.1016/j.molcel.2005.06.007.


Lysidine (2-lysyl cytidine) is a lysine-containing cytidine derivative commonly found at the wobble position of bacterial AUA codon-specific tRNA(Ile). This modification determines both codon and amino acid specificities of tRNA(Ile). We previously identified tRNA(Ile)-lysidine synthetase (tilS) that synthesizes lysidine, for which it utilizes ATP and lysine as substrates. Here, we show that lysidine synthesis consists of two consecutive reactions that involve an adenylated tRNA intermediate. A mutation study revealed that Escherichia coli TilS discriminates tRNA(Ile) from the structurally similar tRNA(Met) having the same anticodon loop by recognizing the anticodon loop, the anticodon stem, and the acceptor stem. TilS was shown to bind to the anticodon region and 3' side of the acceptor stem, which cover the recognition sites. These findings reveal a dedicated mechanism embedded in tRNA(Ile) that controls its recognition and discrimination by TilS, and indicate the significance of this enzyme in the proper deciphering of genetic information.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acyl-tRNA Synthetases / genetics
  • Amino Acyl-tRNA Synthetases / metabolism
  • Codon / chemistry
  • Codon / genetics*
  • Codon / metabolism*
  • Escherichia coli / chemistry
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Kinetics
  • Lysine / analogs & derivatives*
  • Lysine / biosynthesis
  • Molecular Structure
  • Mutagenesis, Site-Directed
  • Protein Conformation
  • Protein Structure, Secondary
  • Pyrimidine Nucleosides / biosynthesis*
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics*
  • RNA, Transfer / metabolism*
  • Time Factors


  • Codon
  • Escherichia coli Proteins
  • Pyrimidine Nucleosides
  • RNA, Transfer
  • lysidine
  • Amino Acyl-tRNA Synthetases
  • tilS protein, E coli
  • Lysine