Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition

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Abstract
Bacterial tyrosyl‐tRNA synthetases (TyrRS) possess a flexibly linked C‐terminal domain of ∼80 residues, which has hitherto been disordered in crystal structures of the enzyme. We have determined the structure of Thermus thermophilus TyrRS at 2.0 Å reso lution in a crystal form in which the C‐terminal domain is ordered, and confirm that the fold is similar to part of the C‐terminal domain of ribosomal protein S4. We have also determined the structure at 2.9 Å resolution of the complex of T.thermophilus TyrRS with cognate tRNAtyr(GΨA). In this structure, the C‐terminal domain binds between the characteristic long variable arm of the tRNA and the anti‐codon stem, thus recognizing the unique shape of the tRNA. The anticodon bases have a novel conformation with A‐36 stacked on G‐34, and both G‐34 and Ψ‐35 are base‐specifically recognized. The tRNA binds across the two subunits of the dimeric enzyme and, remarkably, the mode of recognition of the class I TyrRS for its cognate tRNA resembles that of a class II synthetase in being from the major groove side of the acceptor stem.