Anticodon arm

By observing changes in nucleotides that alter substrate specificity, researchers have identified nucleotide positions that are involved in discrimination by the amino-acyl-tRNA synthetases. These nucleotide positions seem to be concentrated in the amino acid arm and the anticodon arm, including the nucleotides of the anticodon itself, but are also located in other parts of the tRNA molecule. Determination of the crystal structures of aminoacyl-tRNA synthetases complexed with their cognate tRNAs and ATP has added a great deal to our understanding of these interactions (Fig. 27-17). 

Each tRNA has an amino acid arm with the terminal sequence CCA(3 ) to which an amino acid is esterified, an anticodon arm, a Ti//C arm, and a D arm some tRNAs have a fifth arm. The anticodon is responsible for the specificity of interaction between the aminoacyl-tRNA and the complementary mRNA codon. 

Each tRNA has a cloverleaf secondary structure containing an anticodon arm, a D (or DHU) arm, a T or TTC arm, and an amino acid acceptor stem to which the relevant amino acid becomes covalently bound, at the 3 OH group. Some tRNAs also have a variable (or optional) arm. The three-dimensional structure is more complex because of additional interactions between the nucleotides. 

After synthesis, the pre-tRNA molecule folds up into the characteristic stem-loops structures (Fig. 1) and non-tRNA sequence is cleaved from the 5 and 3 ends by ribonucleases. In prokaryotes, the CCA sequence at the 3 end of the tRNA (which is the site of bonding to the amino acid) is enclosed by the tRNA gene but this is not the case in eukaryotes. Instead, the CCA is added to the 3 end after the trimming reactions by tRNA nucleotidyl transferase. Another difference between prokaryotes and eukaryotes is that eukaryotic pre-tRNA molecules often contain a short intron in the loop of the anticodon arm (Fig. 4). 

Fig. 20.8. Three-dimensional structure of phenylalanine specific tRNA from yeast. Watson-Crick type base pairs indicated by slabs, nonstandard base-base interactions that stabilize the tertiary structure are denoted a to h. Invariant and semi-invariant nucleotides are shaded, the four double helical regions are indicated by a a-(amino add) arm, Tarm, D arm, a.c. (anticodon arm [696]...

By chemical and enzymatic probing, the solution structure of this tRNA was analyzed. tRNA is identical to Other tRNAs concerning the T-arm and anticodon arm conformations, and the joining of the D- and T-loops by... 

All tRNA s are similar in structure (Fig. 12.5). The TDC arm participates in binding of the charged tRNA to a site on the ribosome where protein synthesis occurs. The DHU (or D) arm is necessary for recognition by the proper aminoacyl tRNA synthase (the enzyme). The acceptor end is at the 3 terminus and ends in the sequence CAA. The anticodon arm consists of seven nucleotides, the sequence of which is read 3 to 5 (opposite convention to the usual 5 to 3 ). The anticodon sequence is 3 variable base modified purine-X-Y-Z-Py-Py 5. The central bases, X, Y, Z comprise the anticodon, codon 5 ... 

Fig. 4.1 The cloverleaf structure of transfer RNA is shown. The main features of the arms are colored the anticodon arm in green that pairs with messenger RNA during translation, The acceptor stem (red) with the protruding CCA-end to which the activated amino acids are attached...

Figure 4.1 depicts the cloverleaf structure of a tRNA the bars represent base pairs in the stems. There are four arms and three loops - the acceptor, D, T pseudouridine C, and anticodon arms, and D, T pseudouridine C, and anticodon loops. Sometimes tRNA molecules have an extra or variable loop (shown in yellow in Fig. 4.1). The synthesis of transfer RNA proceeds in two steps. The body of the tRNA is transcribed from a tRNA gene. The acceptor stem is the same for all tRNA molecules and added after the synthesis of the main body. It is replaced often during lifetime of a tRNA molecule. The 3-D structure of a yeast tRNA molecule, which can code for the amino acid serine, shows how the molecule is folded with the...

The bonding of the amino acyl-tRNA to the ribosomes occurs via the anticodon arm of the tRNA (see also Figure 29-3). This arm possesses the... 

The general t-RNA structure is characterised by four main arms and a minor extra arm which is of variable size (Figure 11.40). Some unusual bases are always present and about half the nucleotides are base-paired. In addition to the anticodon arm there is the DHU arm which contains up to three dihydrouridine residues, and the T j/C arm containing the T /C sequence of bases. The amino... 

Figure 12.15. Cartoon representations of tRNA. The amino acid arm (shown here bearing an adenosine monophosphate to which the amino acid will be added) as traditionally drawn is across from the anticodon arm, the arm read by the codon of the mRNA attached to the ribosome. The drawing on the left (a) is from PDB ITRA (after Shi, H. Moore, P. B. RNA 2000,6,1091). The drawing on the right (b) is a simplified version of that on the left.

The other arms of the tRNA cloverleaf also have distinctive conserved features. The modified base dihydrouridine (D) is typically present in the loop that closes off a short 3- or 4-bp stem following the acceptor stem. This stem and loop are therefore called the D-arm. The anticodon arm consists of a 5-bp helix closed by a loop that contains the trinucleotide anticodon. Following the anticodon arm is the variable loop, which can contain 3-21 nucleotides, with a stem as long as 7 bp, depending on the particular tRNA. The modified bases pseudouridine (4>) and ribo-thymidine (T) are usually present in the loop of the T FC arm, so named because of the presence of this highly conserved sequence. 

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