Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold

PreQ(1) riboswitches regulate genes by binding the pyrrolopyrimidine intermediate preQ(1) during the biosynthesis of the essential tRNA base queuosine. We report what is to our knowledge the first preQ(1)-II riboswitch structure at 2.3-angstrom resolution, which uses a previously uncharacterized fold to achieve effector recognition at the confluence of a three-way helical junction flanking a pseudoknotted ribosome-binding site. The results account for translational control mediated by the preQ(1)-II riboswitch class and expand the known repertoire of ligand-binding modes used by regulatory RNAs.