Structure of yeast phenylalanine transfer RNA at 2.5 A resolution.

Abstract

The x-ray analysis of the monoclinic form of yeast tRNA~h. has been taken to a resolution of 2.5 A by the method of isomorphous replacement. The model ropsed at 3 A has been confirmed and extended to revea a ditional features of the tertiary structure and of the stereochemistry. An extensive hydrogen bonding network is described involving specific interactions between bases and the ribose-phosphate backbone. The structure of a -U base pair has ben solved.In this paper we present the second stage of the x-ray analysis of the monoclinic form of yeast phenylalanine tRNA. A year ago we proposed a molecular model based on the interpretation of an electron density map at 3 A resolution calculated with phases obtained from isomorphous replacement (1). A similar model was also proposed by Kim et al. (2) for the closely related orthorhombic form. Our map was of sufficient quality to trace the ribose-phosphate chain and to assign all except five nucleotides to peaks in the electron density. These nucleotides lay in a corner of the molecule where the density was strong, but could not be interpreted with as much confidence as the rest of the structure because of tight intra-and intermolecular packing, and two alternative chain tracings were given. In the rest of the molecule we were able to define unambiguously a number of base-base interactions involved in maintaining the tertiary structure, and to describe the extensive stacking interactions present. Many of these interactions could be related to invariances or semiinvariances in the generalized nucleotide sequence of tRNA ( Fig. 1). We showed how other species of tRNA could be accommodated in the same tertiary structure by coordinated changes of sequence (1, 3). The results of a companion study of the chemical reactivity of yeast tRNAPhe were found to be in good accord with the model (4, 5).The x-ray analysis has now been extended to 2.5 A by the method of isomorphous replacement using six heavy atom derivatives to produce an improved electron density map. The structure reported previously (1) has been confirmed and the tracing of the chain in the uncertain region is now unambiguous. The crystallographic discrepancy index, R, has been reduced from 46 to 39%, a value as good as that for protein structure determinations at a comparable stage. The atomic coordinates are unlikely to suffer any large changes in subsequent refinement, and are therefore being published (8).The 2.5 A model allows us to complete the detailed description of base-base interactions in the molecule (Fig. 2). It has also revealed a large number of base-backbone interactions and a new semi-invariant base pair. A hydrogen-bonding network runs through most of the molecule, apart from the exposed amino-acid and anticodon stems. A number of the ribose groups in the nonhelical regions are of the 2'-endo type rather than the 3'-endo found in RNA helices. We now have a picture of the ordered complexity of a folded RNA molecule, a complexity as great as that of a protein. An interesting by-product is...

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