Note: In the PDB file this reference is
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Abstract
Understanding the nature of the free state of riboswitch aptamers is important
for illuminating common themes in gene regulation by riboswitches. Prior
evidence indicated the flavin mononucleotide (FMN)-binding riboswitch aptamer
adopted a 'bound-like' structure in absence of FMN, suggesting only local
conformational changes upon ligand binding. In the scope of pinpointing the
general nature of such changes at the nucleotide level, we performed SHAPE
mapping experiments using the aptamer domain of two phylogenetic variants, both
in absence and in presence of FMN. We also solved the crystal structures of one
of these domains both free (3.3 Å resolution) and bound to FMN (2.95 Å
resolution). Our comparative study reveals that structural rearrangements
occurring upon binding are restricted to a few of the joining regions that form
the binding pocket in both RNAs. This type of binding event with minimal
structural perturbations is reminiscent of binding events by conformational
selection encountered in other riboswitches and various RNAs.
