The structure of the Guanidine-III Riboswitch

We have determined high resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot, in which a connecting strand locates in the major groove of one duplex to form a triple helix. This is continuous with a central core of conserved nucleotides forming a left handed helical ramp of internucleotide interactions that generates the guanidinium cation binding site. The ligand is hydrogen bonded to O6 and N7 of two guanine nucleobases, and to the 2'OH of a cytidine, the nucleobase of which stacks with the guanidinium in a π-cation interaction. The binding pocket has a side opening through which a small side chain can pass, and we have determined structures with bound methylguanidine, aminoguanidine, ethylguanidine and agmatine. Comparison of this structure with those of the guanidine I and II riboswitches reveals common aspects and contrasts.