Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state.

The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown.

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation.

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. We have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer.

FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations.

Knowledge of both apo and holo states of riboswitches aid in elucidating the various mechanisms of ligand-induced conformational "switching" that underpin their gene-regulating capabilities. Previous structural studies on the flavin mononucleotide (FMN)-binding aptamer of the FMN riboswitch, however, have revealed minimal conformational changes associated with ligand binding that do not adequately explain the basis for the switching behavior. We have determined a 2.