CRYSTALLOGRAPHIC REFINEMENT OF YEAST PHENYLALANINE TRANSFER-RNA AT 2.5A RESOLUTION

The crystal structure of yeast tRNAPhe at 2.5 .ANG. resolution was refined, using real-space refinement and improved electron density maps. The refinement confirmed almost all the structural details found earlier by fitting a wire model to the map in an optical comparator. The H-bonding network running through the molecule is described in detail: 41 H-bonds are listed, apart from the 54 in the base-pairs of the double-helical stems. Almost half involve 2''-OH groups of the riboses as acceptors, donors or both. A number of new conformational principles have emerged. Correlations were found between some of the nucleotide torsion angles and the pucker of the ribose ring, and a small number of preferred ways in which a polynucleotide chain can bend or stretch were also determined. The pitch of the double helices in tRNA is less than in RNA fibers (although the other helical parameters are much the same). This is probably a consequence of the different environments of the 2 structures; in tRNA there is evidence for stabilizing interactions between 2''-OH of 1 ribose and 1''-O of its neighbor. The electron density maps give an indication of the degree of thermal motion and disorder in the molecule. The anticodon, the free end of the amino acid stem, and parts of the dhU dihydrouridine and extra loops show only weak density, whereas the T.PSI.C and augmented dhU helices are rigid and have well-defined density.