Tertiary core rearrangements in a tight binding transfer RNA aptamer

Guided by an in vitro selection experiment designed to obtain tight binding aptamers of Escherichia coil glutamine specific tRNA (tRNA(Gln)) for gluta minyl-tRNA synthetase (GlnRS). we have engineered a tRNA mutant in which th e five-nucleotide variable loop sequence 5'-(44)CAUUC(48)-3' is replaced by 5'-(44)AGGU(48)-3'. This mutant tRNA binds to GlnRS with 30-fold improved affinity compared to the wild type. The 2.7 Angstrom cocrystal structure of the RNA aptamer-GlnRS complex reveals major rearrangements in the central tertiary core of the tRNA, while maintaining an RNA-protein interface ident ical to the wild type. The repacked RNA core features a novel hydrogen bond ing arrangement of the trans Levitt pair G15-U48. a new sulfate binding poc ket in the major groove, and increased hydrophobic stacking interactions am ong the bases. These data suggest that enhanced protein binding to a mutant globular RNA can arise from stabilization of RNA tertiary interactions rat her than optimization of RNA-protein contacts.