Anticodon-dihydrouridine stem loop

The results of these efforts show that no method of tRNA recognition is universal.2443 In some cases, e.g., for methionine- or valine-specific tRNAs, the synthetase does not aminoacylate a modified tRNA if the anticodon structure is incorrect. Although the anticodon is 7.5 ran away from the CCA end of the tRNA, the synthetases are large enzymes. Many of them are able to accommodate this large distance between a recognition site and the active site (Fig. 29-9A). For some other tRNAs the anticodon is not involved in recognition 245 For yeast tRNAphe residues in the stem of the dihydrouridine loop and at the upper end of the amino acid acceptor stem seem to be critical.241... 

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. 

The 2-D structure of tRNA, which is generally described by a cloverleaf model, consists of five elements a CCA acceptor stem, a D (dihydrouridine)-loop, an anticodon loop, a variable loop, and a T (ribothymidine)-loop. Tertiary interactions among the secondary structural motifs contribute to the folding that gives rise to the typical L-shaped molecule (Fig. 1.20). X-ray crystallographic structures... 

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