Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNA(Ser) acceptor stem by E-coli seryl-tRNA synthetase

Aminoacylation rate determinations for a series of variant RNA minihelix substrates revealed that Escherichia coli seryl-tRNA synthetase (SerRS) recognizes the 1-72 through 5-68 base pairs of the E.coli tRNA(Ser) acceptor stem with the major recognition elements clustered between positions 2-71 and 4-69. The rank order of effects of canonical base pair substitutions at each position on k(cat)/K-m was used to assess the involvement of major groove functional groups in recognition. Conclusions based on the biochemical data are largely consistent with the interactions revealed by the refined structure of the homologous Thermus thermophilus tRNA(Ser)-SerRS complex that Cusack and colleagues report in the accompanying paper. Disruption of an end-on hydrophobic interaction between the major groove C5(H) of pyrimidine 69 and an aromatic side chain of SerRS is shown to significantly decrease k(cat)/K-m of a minihelix substrate. This type of interaction provides a means by which proteins can recognize the binary information of 'degenerate' sequences, such as the purine-pyrimidine base pairs of tRNA(Ser). The 3-70 base pair is shown to contribute to recognition by SerRS even though it is not contacted specifically by the protein. The latter effect derives from the organization of the specific contacts that SerRS makes with the neighboring 2-71 and 4-69 acceptor stem base pairs.