High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove

Nat Struct Mol Biol. 2019 Dec;26(12):1114-1122. doi: 10.1038/s41594-019-0335-6. Epub 2019 Dec 2.


T-box riboswitches are modular bacterial noncoding RNAs that sense and regulate amino acid availability through direct interactions with tRNAs. Between the 5' anticodon-binding stem I domain and the 3' amino acid sensing domains of most T-boxes lies the stem II domain of unknown structure and function. Here, we report a 2.8-Å cocrystal structure of the Nocardia farcinica ileS T-box in complex with its cognate tRNAIle. The structure reveals a perpendicularly arranged ultrashort stem I containing a K-turn and an elongated stem II bearing an S-turn. Both stems rest against a compact pseudoknot, dock via an extended ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA. Contrary to proposed distal contacts to the tRNA elbow region, stem II locally reinforces the codon-anticodon interactions between stem I and tRNA, achieving low-nanomolar affinity. This study illustrates how mRNA junctions can create specific binding sites for interacting RNAs of prescribed sequence and structure.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Bacterial Proteins / genetics*
  • Binding Sites
  • Crystallography, X-Ray
  • Gene Expression Regulation, Bacterial*
  • Isoleucine-tRNA Ligase / genetics*
  • Models, Molecular
  • Nocardia / genetics*
  • Nucleotide Motifs*
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / metabolism
  • RNA, Transfer, Ile / chemistry*
  • RNA, Transfer, Ile / metabolism
  • Riboswitch / genetics*
  • Structure-Activity Relationship


  • Bacterial Proteins
  • RNA, Bacterial
  • RNA, Transfer, Ile
  • Riboswitch
  • Isoleucine-tRNA Ligase

Supplementary concepts

  • Nocardia farcinica