The three-dimensional structure of yeast phenylalanine tRNA serves as a useful basis for understanding the tertiary structure of all tRNAs. A large number of tRNA sequences have been surveyed and some general conclusions are drawn. There are only a few regions in the molecule in which there are differences in the number of nucleotides; and the structure of yeast phenylalanine tRNA can accommodate these differences by forming or enlarging protuberances on the surface of the basic framework molecule. The nature and distribution of the differences in number of nucleotides are surveyed and possible hydrogen bonding interactions are discussed for a number of tRNA classes. The two most significant features of the molecule are the large number of stacking interactions which are seen to include most of the nucleotides in the molecule and the system of specifie hydrogen bonding interactions. It is likely that these stabilizing elements are preserved in all tRNA structures.Until recently the most striking feature of transfer RNA (tRNA) sequences has been the fact that they could all be arranged in the familiar cloverleaf diagram with complementary hydrogen bonding between the bases in the stem regions (1). In addition, some positions are always occupied by constant nucleotides. Almost 2 years ago, the x-ray diffraction analysis of yeast phenylalanine tRNA (tRNAPhe) at 4-A resolution showed that this molecule not only contains the double helical stems implicit in the cloverleaf diagram, but also was found to have an L shape with the anticodon loop at one end of the L, the acceptor stem at the other end, and the dihydrouracil (D) and TVC loops forming the corner of the molecule (2). More recently the x-ray diffraction analysis of this molecule has been extended to 3-resolution for both the orthorhombic (3, 4) and monoclinic crystal forms (5) and the tertiary interactions in both crystal forms appear very similar.The most striking feature of the 3-A analysis is the extent to which a large number of the bases which are constant to all tRNAs are used in the tertiary hydrogen bonding interactions.These, together with -base stacking, maintain the threedimensional form of the molecule. This suggests rather directly that the three-dimensional structure seen in yeast tRNAPhe may be generalized to understand the structure of all tRNAs. The idea that all tRNAs have a common or similar structure is not surprising in view of the fact that all tRNAs involved in protein synthesis must go through the ribosomal machinery. Here we discuss the manner in which the three-dimensional structure of yeast tRNAPhe may serve as a framework for understanding the structure of all tRNA molecules. We do this by comparing tRNA sequences (6) and suggesting plausible ways in which structural components in this molecule may be modified to fit in other tRNA sequences. Structural features of yeast phenylalanine tRNAThe preliminary details of yeast tRNAPhe tertiary interactions have been published (4, 5). Further improvement of the phases using a "part...

Further analysis of the three-dimensional electron density map of yeast phenylalanine tRNA is presented. Attention is focused on the several types of unique hydrogen bonding that are found in the molecule and a number of sections of the electron density map are presented. These sections are compared with an electron density map of a dinucleoside phosphate. The bases in the helical stem regions are all involved in Watson-Crick hydrogen bonding interactions with the exception of the guanine-uracil base pair. Several additional tertiary hydrogen bonding interactions are described.The specificity in the structure and biological function of the nucleic acids is largely due to the highly specific hydrogen bonding that is found in these molecules. This is especially true for transfer RNA (tRNA). The nucleotide sequences of over seventy tRNAs have been determined, and all of them can be organized in the familiar cloverleaf diagram, which is composed of stems and loops, the stems containing regions in which sequences have complementary bases. Three years ago, the x-ray diffraction analysis of orthorhombic crystals of yeast phenylalanine tRNA at 4 A resolution showed that this tRNA molecule contained the anticipated right-handed, antiparallel double helical regions corresponding to the stems (1). The acceptor and T'C stems of the molecule were found to be approximately colinear and oriented along one arm of an L-shaped molecule, while the dihydrouridine (D) stem and anticodon stems were oriented nearly at right angles to it. These segments were found joined by a complex intertwining of the D loop and the TIC loop. At resolution the ribose-phosphate backbone could be traced, but it was not possible to resolve the additional tertiary hydrogen bonding. That information was revealed last year at 3 A resolution both for the orthorhombic (2) and the monoclinic (3) crystal forms of yeast phenylalanine tRNA. These two analyses were very similar, except that the electron density map of the monoclinic crystal was not sufficiently resolved to interpret the tertiary interactions that hold the D-loop and T'C loop together. We have continued our analysis of the orthorhombic crystals of yeast phenylalanine tRNA and presently have diffraction data to a resolution of 2.5 A. We have examined in considerable detail the electron density map that was constructed using the multiple isomorphous replacement (MIR) method. Here we document a large number of the hydrogen bonding interactions in yeast phenylalanine tRNA by presenting the MIR electron density maps at 3 A resolution together with the interpretations that we have placed on this map. In the course of this analysis we have confirmed the hydrogen bonding interactions that were described approximately a year ago (2) and have also discovered some additional interactions that further stabilize the three-dimensional structure of this tRNA. MATERIALS AND METHODSThe methods for preparing crystals of orthorhombic yeast phenylalanine tRNA have been described (4, 5). The electron density m...