Three-dimensional Structure Of tRNA Research Articles

Domain-domain communication in a miniature archaebacterial tRNA synthetase.

The three-dimensional structure of tRNA is organized into two domains-the acceptor-TPsiC minihelix with the amino acid attachment site and a second, anticodon-containing, stem-loop domain. Aminoacyl-tRNA synthetases have a structural organization that roughly recapitulates the two-domain organization of tRNAs-an older primary domain that contains the catalytic center and interacts with the minihelix and a secondary, more recent, domain that makes contacts with the anticodon-containing arm. The latter contacts typically are essential for enhancement of the catalytic constant k(cat) through domain-domain communication. Methanococcus jannaschii tyrosyl-tRNA synthetase is a miniature synthetase with a tiny secondary domain suggestive of an early synthetase evolving from a one-domain to a two-domain structure. Here we demonstrate functional interactions with the anticodon-containing arm of tRNA that involve the miniaturized secondary domain. These interactions appear not to include direct contacts with the anticodon triplet but nonetheless lead to domain-domain communication. Thus, interdomain communication may have been established early in the evolution from one-domain to two-domain structures.

Chemical modification study of aminoacyl-tRNA conformation

Chemical reactivity of cytosines in 32P-labeled E. coli tRNA1Leu, E. coli tRNAPhe and yeast tRNAPhe before and after aminoacylation was examined by use of a cytosine-specific reagent, semicarbazide-bisulfite mixture. In all the three tRNA species examined, the cytosine residues that were susceptible to the modification were the same in the aminoacylated tRNA and the unacylated tRNA. Only a limited number of the cytosine residues were modifiable: those that occur in the anticodon, the 3'-CCA terminus, the D-loop, and the extra loop. The sites accessible by the reagent are in good agreement with the general three-dimensional structure of tRNA proposed in literature. These results indicate that the gross conformation of these tRNAs does not change on aminoacylation, and consequently favor the view that the T psi C(G) sequence could become exposed in later steps of protein synthesis in order to achieve the binding of aminoacyl tRNA to ribosomes.

Specificity in the Structure of Transfer RNA

This chapter discusses the recent work on the specificity embodied in the structure of transfer RNA (tRNA). The chapter also discusses the base composition of tRNA. The numerous analyses of the base composition of bulk tRNA preparations from different sources have been reviewed in this chapter. The various arrangements of nucleotides in tRNA are also discussed in this chapter. Counter-current distribution, column chromatography, and other separation techniques have been used in the fractionation of tRNA's. Some of them are highly specific for one particular amino acid. The base composition of these fractionated tRNA's is characteristic. The arrangement of nucleotides in tRNA, such as (a) nucleotide distribution, (b) anticodon sequence, and (c) terminal nucleotide sequences, are discussed in this chapter. Although a definite tertiary structure of tRNA has not yet been defined, each specific tRNA, which has a specific base composition, may have a specific tertiary configuration, because the melting profiles of a few specific tRNA's differ from each other. The chapter also describes various three-dimensional structure of tRNA. The chapter concludes with the modification of nucleic acid bases, without scission of the polynucleotide chain, and the resulting change in the biological activities of nucleic acids from viruses or bacteria. In order to elucidate the functional sites of tRNA, it seems logical to examine the change in the activity of such modified tRNA.