Structural basis for recognition of G-1-containing tRNA by histidyl-tRNA synthetase

Nucleic Acids Res. 2015 Mar 11;43(5):2980-90. doi: 10.1093/nar/gkv129. Epub 2015 Feb 26.


Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in protein translation by linking tRNAs with cognate amino acids. Among all the tRNAs, only tRNA(His) bears a guanine base at position -1 (G-1), and it serves as a major recognition element for histidyl-tRNA synthetase (HisRS). Despite strong interests in the histidylation mechanism, the tRNA recognition and aminoacylation details are not fully understood. We herein present the 2.55 Å crystal structure of HisRS complexed with tRNA(His), which reveals that G-1 recognition is principally nonspecific interactions on this base and is made possible by an enlarged binding pocket consisting of conserved glycines. The anticodon triplet makes additional specific contacts with the enzyme but the rest of the loop is flexible. Based on the crystallographic and biochemical studies, we inferred that the uniqueness of histidylation system originates from the enlarged binding pocket (for the extra base G-1) on HisRS absent in other aaRSs, and this structural complementarity between the 5' extremity of tRNA and enzyme is probably a result of coevolution of both.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aminoacylation
  • Base Sequence
  • Catalytic Domain
  • Crystallography, X-Ray
  • Guanine / chemistry*
  • Guanine / metabolism
  • Histidine-tRNA Ligase / chemistry*
  • Histidine-tRNA Ligase / genetics
  • Histidine-tRNA Ligase / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation*
  • Protein Binding
  • Protein Structure, Tertiary*
  • RNA, Transfer, His / chemistry*
  • RNA, Transfer, His / genetics
  • RNA, Transfer, His / metabolism
  • Sequence Homology, Amino Acid
  • Thermus thermophilus / enzymology
  • Thermus thermophilus / genetics


  • RNA, Transfer, His
  • Guanine
  • Histidine-tRNA Ligase