The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation

Proc Natl Acad Sci U S A. 1998 Jan 20;95(2):460-5. doi: 10.1073/pnas.95.2.460.


We have identified six new aminoacylation determinants of Escherichia coli tRNAGln in a genetic and biochemical analysis of suppressor tRNA. The new determinants occupy the interior of the acceptor stem, the inside corner of the L shape, and the anticodon loop of the molecule. They supplement the primary determinants located in the anticodon and acceptor end of tRNAGln described previously. Remarkably, the three-dimensional structure of the complex between tRNAGln and glutaminyl-tRNA synthetase shows that the enzyme interacts with the phosphate-sugar backbone but not the base of every new determinant. Moreover, a small protein motif interacts with five of these determinants, and it binds proximal to the sixth. The motif also interacts with the middle base of the anticodon and with the backbones of six other nucleotides. Our results emphasize that synthetase recognition of tRNA is more elaborate than amino acid side chains of the enzyme interacting with nucleotide bases of the tRNA. Recognition also includes synthetase interaction with tRNA backbone functionalities whose distinctive locations in three-dimensional space are exquisitely determined by the tRNA sequence.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acylation
  • Amino Acyl-tRNA Synthetases
  • Base Sequence
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Glycine-tRNA Ligase / genetics
  • Glycine-tRNA Ligase / metabolism*
  • Molecular Sequence Data
  • Molecular Structure
  • RNA, Bacterial / metabolism*
  • RNA, Transfer
  • RNA, Transfer, Gln / genetics
  • RNA, Transfer, Gln / metabolism*


  • RNA, Bacterial
  • RNA, Transfer, Gln
  • RNA, Transfer
  • Amino Acyl-tRNA Synthetases
  • Glycine-tRNA Ligase