Structure of tRNAs

FIGURE 12.34 A general diagram for the structure of tRNA. The positions of invariant bases as well as bases that seldom vary are shown in color. The numbering system is based on yeast tRNA R = purine Y= pyrimidine. Dotted lines denote sites in the D loop and variable loop regions where varying numbers of nucleotides are found in different tRNAs. 

G. Dirheimer G. Keith A.-P. Sibler R. P. Martin, The Primary Structure of tRNAs and Their Rare Nucleosides. In Transfer RNA Structure, Properties, and Recognition, P. Schimmel, D. Soil, J. N. Abelson, Eds. Cold Spring Harbor Laboratory Cold Spring Harbor, NY, 1979 Vol. 9A, pp 19-41. 

In mid-1997 an international conference took place in Santa Cruz, USA, in which, for the first time, the exclusive topic was structural aspects of RNA molecules. A report covering this meeting contains an impressive graphic which shows the RNA structures, RNA/DNA complexes, and RNA/protein complexes contained in the brookhaven database as a function of the year of their publication [29]. Between 1988 and 1993 there were just 20. However, in 1996 alone no less than 41 structures appeared. These new dimensions were headed by the crystal structural elucidation of the first larger RNA molecule since the first crystal structure of tRNA in 1973 [30], the 48 nucleotide long hammerhead ribo-zyme (HHR) [31-33]. This landmark achievement was followed by a crystal structure analysis of the P4-P6-domain of a group I intron [34-36] and, more recently, a crystal structure of the hepatitis delta virus ribozyme [37]. 

The clover-leaf pattern of Figure 25-26 shows the general structure of tRNA. There are regions of the chain where the bases are complementary to one another, which causes it to fold into two double-helical regions. The chain has three bends or loops separating the helical regions. 

With this information on the structure of tRNA, we can proceed to a discussion of the essential features of biochemical protein synthesis. 

FIGURE 3.7 A cryo-EM map of the Escherichia coli ribosome (complexed with fMet-tRNAf Met and mRNA) where fMet = formylmethionine obtained from 73,000 particles at a resolution of 11.5 A. (a-d) Four views of the map, with the ribosome 30S subunit painted in yellow, the ribosome 50S subunit in blue, helix 44 of 16S RNA in red, and fMet-tRNA at the P site in green. Inset on top juxtaposes the experimental tRNA mass (green, on left) with the appearance of the X-ray structure of tRNA at 11 A resolution (on right). Arrows mark points at which tRNA contacts the surrounding ribosome mass. Landmarks h = head and sp = spur of the 30S subunit. CP = central protuberance LI = LI stalk and St = L7/L12 stalk base of the 50S subunit. 

The three dimensional structure of tRNA (Fig. lb) is even more complex because of additional interactions between the various units of secondary structure. 

While RNA molecules usually exist as single chains, they often form hairpin loops consisting of double helices in the A conformation (Moore, 1999). The best-known forms of RNA are the low-molecular-weight tRNA molecules. In all of them the bases can be paired to form a cloverleaf structure with three hairpin loops and sometimes a fourth. The cloverleaf structure of tRNA is further folded into an T-shape conformation with the anticodon triplet and the aminoacyl attachment CCA forming the two ends. 

RNA molecules form secondary structure by folding their polynucleotide chains via hydrogen bond formations between AU pairs and GC pairs. The thermochemical stability of forming such hydrogen bonds provides useful criterion for deducing the cloverleaf secondary structure of tRNAs that is, tRNA molecules are folded into DFI... 

You can see the common structural features of tRNAs at both the secondary and tertiary levels. Only a few sequences or bases are common to all tRNAs. The common secondary structure of tRNAs is the cloverleaf pattern, where the 5 and 3 sequences are base-paired, and then the other three stem-loops of the cloverleaf are formed by... 

The tertiary structure of all tRNAs are likewise similar. All known tRNAs are roughly L-shaped, with the anticodon on one end of the L and the acceptor stem on the other. Each stem of the L is made up of two of the stems of the cloverleaf, arranged so that the base pairs of each stem are stacked on top of each other. The parts of the molecule that are not base-paired are involved in other types of interactions, termed tertiary interactions. The tertiary structures of tRNAs thus reflect the dual functions of the molecule The anticodons are well-separated from the acceptor stems. This feature allows two tRNA molecules to interact with two codons that are adjacent on an mRNA molecule. See Figure 10-4. 

Figure 17-7 is a diagrammatic representation of tRNA folded into the typical cloverleaf structure, containing a number of stems (base-paired) and loops. While the sequences of the different tRNAs are different, there are regions that remain invariant. Most of these are in the loops, within which the unusual bases are concentrated, and at the 3 end of the molecule contained within the acceptor stem. The sequence at this end is always CCA, and it is to the 3 OH that the appropriate amino acid is attached through its carboxyl group. The three nucleotides complementary to the codon for the amino acid make up what is known as the anticodon (shaded part of Fig. 17-7). The three-dimensional structure of tRNA is known. In this structure, there are additional H bonds, which stabilize the cloverleaf in a more elongated L-shaped structure, with the acceptor sequence at one end and the anticodon loop at the other.

Fig. 17-7 A diagrammatic representation of the folded cloverleaf structure of tRNA.

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

The secondary clover-leaf structure of tRNA is stabilized by Watson-Crick base pairs. The tRNA s are a large family of molecules consisting of 71 to 76 nucleotides, with about 10% of rare bases (Fig. 15.2). The known nucleotide sequences of over 200 tRNA s [695J can be arranged in a characteristic clover-leaf model with four double helical stems and three loop regions. In some of the positions, the same nucleotide occurs, called invariant, in others only the type is conserved, i.e.,... 

Moras D (1989) Crystal structures of tRNAs. In Saenger W (ed) Nucleic acids. Landolt-BOrnstein New Series group VII. Biophysics, vol. lb. Springer, Berlin, pp 1-30... 

Figure 5 Protein-RNA interactions of aaRSs. The cloverleaf secondary structure of tRNA " folds into an L-shaped tertiary molecule. The tRNA can bind in an aminoacylation complex, where the 3 end is located in the canonical Class I or Class II core as shown in the upper right for the P. horikoshii LeuRS-tRNA - aminoacylation complex. In aaRSs that edit, a second complex can be formed, where the 3 end interacts with a separate domain such as the connective polypeptide insertion (CPI) that contains a hydrolytic active site as shown in the lower right for the T. thermophilus LeuRS-tRNA - editing complex. (Table (1) PDB files 1WZ2 and 2BYT).

Figure 29.4. General Structure of tRNA Molecules. Comparison of the base sequences of many tRNAs reveals a number of conserved features.

Figure 29.6. Helix Stacking in tRNA. The four helices of the secondary structure of tRNA (see Figure 29,4) stack to form an L-shaped structure.

The structure of t (transfer) and r(ribosomal) RNA consists of multiple, single stranded, stem-loop structures. The stems consist of helices formed by base pairing of complementary regions within the RNA. The secondary structure of tRNA and rRNA are important for their biological functions, mRNA also assumes some degree of secondary structure but not to the same extent as tRNA and rRNA. 

Figure 3-12. The cloverleaf structure of tRNA. Bases that commonly occur in a particular position are indicated by letters. Base-pairing in stem regions is indicated by lines between strands, xy = pseudouridine T = ribothymi-dine D = dihydrouridine.

It must be appreciated that the foregoing is only a skeletal account of a very complex process involving initiation factors, elongation factors and release factors. In addition, the remarkable structures of tRNAs have not been discussed here. 

Fig. 20. Two of the binding sites that are important in folding of tRNAP are targeted by Ru(tpy)(bpy)0, as indicated by the solid arrows. Crystal structure of tRNA " taken from Jack et al. (67).

Vlassov, V.V., Giege, R. and Ebel, J.P. (1981). Tertiary structure of tRNAs in solutions monitored by phosphodiester modification with ethylni-trosourea. Eur. J. Biochem. 119, 51-59. 

Transfer RNA (tRNA) molecules transport amino acids to ribosomes for assembly into proteins. Comprising about 15% of cellular RNA the average length of a tRNA molecule is 75 nucleotides. Because each tRNA molecule becomes bound to a specific amino acid, cells possess at least one type of tRNA for each of the 20 amino acids commonly found in protein. The three-dimensional structure of tRNA molecules, which resembles a warped cloverleaf (Figure 17.22), results primarily from extensive intrachain base pairing. tRNA molecules contain a variety of modified bases. Examples include pseudouridine, 4-thiouridine, 1-methylguanosine, and dihydrouridine ... 

The structure of tRNA allows it to perform two critical functions involving the most important structural components the 3 -terminus and the anticodon loop. 

The Folded Structure of tRNA Promotes Its Decoding Functions... 

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