Crystallographic refinement of yeast aspartic acid transfer RNA

A three‐dimensional structure model of the complex of glutamyl‐tRNA synthetase and its cognate tRNA

“…it has four nucleotide residues, in contrast to the five found in most tRNAs, such as E. coli tRNA GIn and yeast tRNA Phe. The number of nucleotides in the variable loop is expected to influence the 3D structure of the 'augmented D helix', which is composed of the D stem, the variable loop, and their neighboring nucleotide residues [15,191. In addition, the conformation of the augmented D helix of tRNA G~u could, essentially, be conserved through interactions with GIuRS.…”

“…The coordinates of the anticodon arm of yeast tRNA Ph° [14], and those of the D-and T-arms, and the variable loop of yeast tRNA A~p [15] were obtained form the Brookhaven Protein Data Bank [16].…”

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis

“…base-pair G26:A44 in tRNA Asp (Westhof et al, 1985) and in the P4-P6 domain of group I introns (Cate et al, 1996a). Similarly, A:C pairs are observed at the edge of RNA helices; for example, an A:C pair is found at the edge of the anticodon stem of tRNA Asp (Westhof et al, 1985). Therefore, the presence of purine:purine or A:C pairs at the base of P19 is fully compatible with the extension of the helical stack.…”

“…Purine:purine pairs have been observed in crystallographic structures extending regular helical stems, e.g. base-pair G26:A44 in tRNA Asp (Westhof et al, 1985) and in the P4-P6 domain of group I introns (Cate et al, 1996a). Similarly, A:C pairs are observed at the edge of RNA helices; for example, an A:C pair is found at the edge of the anticodon stem of tRNA Asp (Westhof et al, 1985).…”

Higher-order structure of bovine mitochondrial tRNASerUGA: chemical modification and computer modeling

“…Almost all tRNAs from prokaryotes and eukaryotic cytoplasms possess the highly conserved cloverleaf secondary structure (1,2), which is further folded into the common L-shaped tertiary structure (3)(4)(5)(6)(7)(8). However, it has been inferred from their gene sequences that a number of animal mitochondrial (mt) tRNAs possess unusual secondary structures, presumably due to a lack of invariant nucleotides necessary for forming terdary interactions (1).…”