Yeast phenylalanine tRNA

Page 1176 (Figure 28 11) is adapted from crystallographic coordinates deposited with the Protein Data Bank PDB ID 6TNA Sussman J L Holbrook S R Warrant R W Church G M Kim S H Crystal Structure of Yeast Phenylalanine tRNA I Crystallographic Refinement / Mol Biol 1978 126 607 (1978)... 

FIGURE 12.37 Tertiary interactions in yeast phenylalanine tRNA. The molecnle is presented in the conventional cloverleaf secondary strnctnre generated by intrastrand hydrogen bonding. Solid lines connect bases that are hydrogen-bonded when this cloverleaf pattern is folded into the characteristic tRNA tertiary strnctnre (see also Figure 12.36). 

Figure 5-34 (A) Two conformations of a segment of the yeast phenylalanine tRNA gene. The segment shown codes for the 3 end of the tRNA molecule shown in Fig. 5-30, including the T /C loop. (B) Formation of H-DNA (Fig. 5-24) proposed for a sequence in plasmid pGG32. The major element of the structure is the triplex, which is formed from the Watson-Crick duplex ( ) associated with the homopyrimidine loop through Hoogsteen base pairing (o, +). One of the two possible "isomeric" forms is shown. See Mirkin et al.378...

The tertiary structure of yeast phenylalanine tRNA. (a) The full tertiary structure. Purines are shown as rectangular slabs, pyrimidines as square slabs, and hydrogen bonds as lines between slabs. (Source From G. J. Quigley and A. Rich, Structural domains of transfer RNA molecules, Science, 194 796, 1976.) (b) Nucleotide sequence. Residues... 

When yeast phenylalanine tRNA is digested with a small amount of RNase (partial digest) such as T2 RNase, almost all of the cleavage sites are found in the anticodon loop. Explain this observation. 

FIGURE 10.1 An electron density map section from a yeast phenylalanine tRNA crystal showing contour lines drawn about areas of high electron density. In the map can be seen what appear to be broken lengths of continuous chains of density. When electron density sections above and below are included, the chains assume greater continuity. 

FIGURE 10.15 A model of yeast phenylalanine tRNA built according to an electron density map computed using 2.8 A resolution X-ray data. The model is constructed of Kendrew parts connected together by tiny screws. It required several months to build and is roughly 6 feet by 4 feet by 3 feet in size. It was constructed at MIT in 1972 by the author. 

FIGURE 27.28 Phenylalanine tRNA. (a) A schematic drawing showing the sequence of bases. RNAs usually contain modified bases (green boxes), slightly different from those in other RNAs. The anticodon for phenylalanine is shown in red, and the CCA triplet which bears the phenylalanine is in blue. (6) The experimentally determined structure for yeast phenylalanine tRNA. Complementary base-pairing is present in some regions, but not in others. 

R. S. Brown, ]. C. Dewan and A. Klug, Crystallographic and biochemical investigation of the lead (11)-catalyzed hydrolysis of yeast phenylalanine tRNA, Biochemistry 1985, 24, 4785-4801 (pdb ltn2). 

FIGURE 9.24 The three-dimensional structure of yeast phenylalanine tRNA as deduced from X-ray diffraction studies of its crystals. The tertiary folding is illustrated, and the ribose-phosphate backbone is presented as a continuous ribbon ff bonds are indicated by crossbars. Unpaired bases are shown as short, unconnected rods. The anticodon loop is at the bottom and the —CCA 3 —OH acceptor end is at the top right. 

In addition to the relatively regular triplexes, base triads occur in many RNA structures. Within the last decade, RNA structural biology has come of age and now provides a rapidly increasing number of new structures with rather different structural motifs. Therefore, RNA structures represent a treasury of higher-order base complexes. It is very likely that the first base triads ever seen at atomic detail are fi-om yeast phenylalanine tRNA. Fig. 4 shows three base triads located in the central part of this structure. The ribosomal subunits (PDB codes Iffk, l f, l g) contain of course a rather large number of base triads. " However, small structures of pseudoknots, aptamers and ribozymes may also include more than one triad. For example, the... 

A space-filling model of yeast phenylalanine tRNA. (Image of 1EHZ(H. Shi,... 

The sequence of the approximately 75 nucleotide residues has been determined for many different tRNA molecules. In all of them there are the same four sequences of complementary pairs A=U or G=C, as shown in Figure 15-25. The existence of these sequences permitted the inference to be drawn that the molecule has the clover-leaf structure shown in Figure 15-25. This structure has been verified by an x-ray-diffraction study of crystals of yeast phenylalanine tRNA, with the result shown in Figure 15-26. 

Schematic representation of the three-dimensional structure of yeast phenylalanine tRNA, as found by an x-ray-diifraction study of crystals of the substance. There are 76 nucleotides in the tRNA chain. Hydrogen bonds are represented by rods. (S. H. Kim, F. L. Suddath. G. J. Quigley, A. MacPherson, J. L. Sussman. A. H. J. Wang. N. C. Seeman, and A. Rich, Science 185, 435 (1974).] Copyright 1974 by the American Association for the Advancement of Science.

Fig. 1. Cloverleaf diagram of yeast phenylalanine tRNA (tRNA ). Bases enclosed in solid or dashed squares are constant for all tRNAs active in chain elongation. Solid lines indicate tertiary interactions between bases and involve one, two or three hydrogen bonds. The regions a and p in the D loop contain from I to 3 nucleotides in different tRNA sequences [81T3].

D, 5,6-dihydrouridine. (b) The three-dimensional conformation of yeast phenylalanine tRNA... 

L. Jovine, S. Djordjevic, and D. Rhodes, J. Molec. Biol., 301, 401 (2000). The Crystal Structure of Yeast Phenylalanine tRNA at 2.0 A Resolution Cleavage by Mg in 15-Year Old Crystals. 

Fig. 11. Temperature dependence of the P chemical shift of the double-helix signal of the 1 1 mixture of oligouiidylic acid [oIigo(U)] and polyadenylic add (poly(A)] (O, —) and P signals of yeast phenylalanine-tRNA (—). For poly(A) oligo(U) sample pH 7, 20% D2O, 0.2 NaCl, 10 mMcacodylate, 1 mil/EDTA. 24 mg/ml total nucleotide. For tRNA 0.1 M NaQ, 10 mM cacodylate, 10 mMMgQ2,1 mAf EDTA, 10-20% D2O, pH 7. From Gorenstein, et al. (1982). Copyright 1982 American Chemical Sodety.

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