Solution Conformations of Unmodified and A37N6-dimethylallyl Modified Anticodon Stem-loops of Escherichia coli tRNAPhe

Identification of determinants for tRNA substrate recognition byEscherichia coliC/U34 2′-O-methyltransferase

“…Indeed, it was reported that the i 6 A37 modification changes the structural conformation of E. coli tRNA Phe GAA ASL, as observed in NMR structures. 49 The unmodified ASL molecule adopts a stem-loop conformation composed of 7 base-pairs and a compact 3 nucleotide loop, which is obviously different from the classical loop observed in fully modified tRNA which contains a U-turn motif at position 33. 49 Therefore, the conformational change of ASL resulting from the i 6 A37 modification might also be important for recognition by TrmL.…”

Purine bases at position 37 of tRNA stabilize codon–anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions

“…The principal function of modified nucleosides seems to ensure the correct conformation of the three anticodon residues in the context of a seven-nucleotide loop to allow for correct reading of the codon (Yokoyama and Nishimura 1995). The structural influence of modified nucleotides can be quite significant, particularly when the modifications are required to stabilize a canonical U-turn structure of the loop, as shown for tRNA Lys (Agris 1996;Stuart et al 2000;Sundaram et al 2000) or E. coli tRNA Phe (Cabello-Villegas et al 2002). In other cases, exemplified by tRNA Asp (Perret et al 1990), the lack of modifications has little effect on the structure of the anticodon loop, whereas the interactions stabilizing the elbow region may be altered.…”

Solution structure of the pseudo-5′ splice site of a retroviral splicing suppressor

“…The initial NRS structure was calculated using a reported protocol (Cabello-Villegas et al 2002). The constraints included 423 distance restraints, among which 377 are NOE constraints, 46 hydrogen bond constraints, and 63 torsion angle restraints.…”