Structural analogies between the 3′ tRNA‐like structure of brome mosaic virus RNA and yeast tRNA Tyr revealed by protection studies with yeast tyrosyl‐tRNA synthetase

Contacts between the tRNA‐like domain in brome mosaic virus RNA and yeast tyrosyl‐tRNA synthetase have been determined by footprinting with enzymatic probes. Regions in which the synthetase caused protections indicative of direct interaction coincide with loci identified by mutational studies as being important for efficient tyrosylation [Dreher, T. W. & Hall, T. C. (1988) J. Mol. Biol. 201 , 41–55]. Additional extensive contacts were found upstream of the core of the tRNA‐like structure. In parallel, the contacts of yeast tRNA Tyr with its cognate synthetase were determined by the same methodology and comparison of protected nucleotides in the two RNAs has permitted the assignment of structural analogies between domains in the viral tRNA‐like structure and tRNA Tyr . Amino acid acceptor stems are similarly recognized by yeast tyrosyl‐tRNA synthetase in the two RNAs, indicating that the pseudoknotted fold in the viral RNA does not perturb the interaction with the synthetase. A further important analogy appears between the anticodon/D arm of the L‐conformation of tRNAs and a complex branched arm of the viral tRNA‐like structure. However, no apparent anticodon triplet exists in the viral RNA. These results suggest that the major determinants for tyrosylation of yeast tRNA Tyr lie outside the anticodon stem and loop, possibly in the amino acid acceptor stem.