N

-N Ribose

N6- (threoninocarbonyl) adenosine (t6A)

NHCOOCH3 CHCOOCH3 CH2

NHCOOCH3 CHCOOCH3 CH2

Wybutosine (yW or Y)

Figure 3.4. Some hypermodified nucleosides occurring in the position adjacent to the anticodon at its 3'-side.

Wybutosine (yW or Y)

Figure 3.4. Some hypermodified nucleosides occurring in the position adjacent to the anticodon at its 3'-side.

Structurally, the paired (double-stranded) part of each arm of tRNA is a double helix. The RNA double helix contains 11 pairs of nucleotide residues per turn. The parameters of this helix are similar to hose of the A-form of DNA. The double helix is the main element of tRNA secondary structure. In addition to the canonical Watson-Crick base pairs G:C and A:U, the double-stranded regions of tRNA often contain the G:U pair, which is close by its steric parameters to the canonical pairs (Fig. 3.5).

The secondary structure of unpaired regions, such as loops and the acceptor ACCA- or GCCA terminus, is of a different type. A single-helical arrangement of several residues maintained by base-stacking interactions can occur here. The structure of the anticodon loop is particularly interesting (Fig. 3.6); three anticodon bases and two subsequent bases adjacent to the anticodon from the 3'-side are stacked with each other and form a single-stranded, right-handed helix; the first base of the anticodon is located at the top of the helix, and the groups capable of forming hydrogen bonds of all three anticodon bases are exposed outward. Such an orientation of the anticodon bases is extremely important for interaction with the mRNA codon. The features of the primary structure of the anticodon loop contribute specifically to the maintenance of the spatial arrangement described: the hypermodified purine base directly adjacent to the anticodon from the 3'-side as well as the next base, usually also a purine, provides for stable stacking interactions in the single-stranded helix, while the two "small" pyrimidine bases at the 5'-side of the anticodon, and particularly the adjacent invariant U, make a sharp bend in the chain (between the anticodon and U) and

Figure 3.5. Base pairing in RNA double helices: ball-and-stick drawing. Top to bottom, A:U and U:A; G:C and C:G; G:U and U:G. Solid circles are carbons, shaded circles - nitrogens, large open circles - oxygens, and small open circles - hydrogens; solid sticks are N-glycosidic bonds between the base and ribose.

Figure 3.5. Base pairing in RNA double helices: ball-and-stick drawing. Top to bottom, A:U and U:A; G:C and C:G; G:U and U:G. Solid circles are carbons, shaded circles - nitrogens, large open circles - oxygens, and small open circles - hydrogens; solid sticks are N-glycosidic bonds between the base and ribose.

Yeast Trna Phenylalanine

Figure 3.6. Anticodon loop of yeast phenylalanine tRNA: ball-and-stick skeletal model without hydrogens. The path of the backbone is given in solid black; three anticodon residues are shaded. (The three-dimensional structure of the yeast tRNAPhe is determined by X-ray crystallography: S.-H. Kim, F.L. Suddath, G.J. Quigley, A. McPherson, J.L. Sussman, A. H.-J. Wang, N.C. Seeman & A. Rich, Science 185, 435-440, 1974; J.D. Robertus, J.E. Ladner, J.T. Finch, D. Rhodes, R.S. Brown, B.F.C. Clark & A. Klug, Nature 250, 546-551, 1974).

Figure 3.6. Anticodon loop of yeast phenylalanine tRNA: ball-and-stick skeletal model without hydrogens. The path of the backbone is given in solid black; three anticodon residues are shaded. (The three-dimensional structure of the yeast tRNAPhe is determined by X-ray crystallography: S.-H. Kim, F.L. Suddath, G.J. Quigley, A. McPherson, J.L. Sussman, A. H.-J. Wang, N.C. Seeman & A. Rich, Science 185, 435-440, 1974; J.D. Robertus, J.E. Ladner, J.T. Finch, D. Rhodes, R.S. Brown, B.F.C. Clark & A. Klug, Nature 250, 546-551, 1974).

maintain the loop conformation, particularly at the expense of a hydrogen bond between the invariant U and the phosphate group of the third residue of the anticodon.

3.2.3. Tertiary Structure

The three-dimensional structure of tRNA was. first reported for yeast tRNAPhe. This structure was determined independently by the groups of Alexander Rich and Aaron Klug in 1974 through the use of X-ray analysis of tRNAPhe crystals (Kim et al., 1974; Robertus et al., 1974). A great deal of indirect evidence as well as direct determinations of the three-dimensional structures of several other tRNA species has demonstrated that the main pattern of tRNA chain folding into the tertiary structure is universal. Schematically, this folding may be represented as follows. The acceptor stem and the T-arm are arranged along a common axis, forming a continuous double helix of 12 nucleotide pairs in length; the anticodon arm and the dihydrouridylic arm are also arranged along a common axis and yield another double helix, this one 9 nucleotide pairs long. These two helices are oriented toward each other at approximately a right angle so that the dihydrouridylic loop is brought into proximity with the T-loop, and the interaction between the GG invariant and the YC invariant fastens them together (Fig. 3.7). As a result, the structure looks like the letter L with the tops of its two limbs corresponding to the anticodon and the acceptor 3'-end. The short, single-stranded bridge between the acceptor stem and dihydrouridylic helix (residues 8 and 9), part of the dihydrouridylic loop, and the additional variable loop are superimposed on the dihydrouridylic helix in the region of the inner corner of the L-shaped molecule, resulting in the formation of the so-called core of the molecule with a number of tertiary interactions. In a schematic drawing of the model of the

AC arm

AC arm

G hU hU

0 0

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