A distinctive RNA fold: The solution structure of an analogue of the yeasttRNA(Phe) T psi C domain

The structure of an analogue of the yeast tRNA(Phe) T Psi C stem-loop has b een determined by NMR spectroscopy and restrained molecular dynamics. The m olecule contained the highly conserved modification ribothymidine at its na turally occurring position. The ribothymidine-modified T Psi C stem-loop is the product of the m(5)U(54)-tRNA methyltransferase, but is not a substrat e for the m(1)A(58)-tRNA methyltransferase. Site-specific substitutions and N-15 labels were used to confirm the assignment of NOESY cross-peaks criti cal in defining the global fold of the molecule. The structure is unusual i n that the loop folds far over into the major groove of the curved stem. Th is conformation is stabilized by both stacking interactions and hydrogen bo nd formation. Furthermore, this conformation appears to be unique among RNA hairpins of similar size. There is, however, a considerable resemblance to the analogous domain in the crystal structure of the full-length yeast tRN A(Phe). We believe, therefore, that the structure we have determined may re present an intermediate in the folding pathway during the maturation of tRN A.