Association of tRNA(Gln) acceptor identity with phosphate-sugar backbone interactions observed in the crystal structure of the Escherichia coli glutaminyl-tRNA synthetase-tRNA(Gln) complex.

We isolated several mutants with nucleotide substitutions in alanine tRNA (tRNA(Ala)) that resulted in glutamine tRNA (tRNA(Gln)) acceptor identity in Escherichia coli. These substitutions were in three regions of tRNA structure not previously associated with tRNA(Gln) acceptor identity. Only the phosphate-sugar backbone moieties of these nucleotides interact with the enzyme in the previously determined X-ray crystal structure of the complex between tRNA(Gln) and glutaminyl-tRNA synthetase. We conclude that these sequence-dependent phosphate-sugar backbone interactions contribute to tRNA(Gln) identity, and argue that the interactions help communicate enzyme recognition of the anticodon to the acceptor end of the tRNA and the catalytic center of the enzyme.