(A) An overlay of the three riboswitches in the ligand-bound state shows nearly overlapping structural scaffolds. (B) The cartoon schematic of the ykkC riboswitch motif and subtypes highlights the shared structural core of the guanidine-I (top), PRPP (middle), and ppGpp (bottom) riboswitches. Ligand selectivity for PRPP and ppGpp is conferred by an additional helical element (dashed lines). The corresponding consensus secondary structures are adapted from [18] and [11]. Crystal structures are shown with co-ordinated Mg²⁺ ions as spheres and ligands as ball and stick models (pdb codes: 5T83, 6DLT, and 6DMC, from [8] and [18]). Assessing the individual active site structures shows that PRPP and ppGpp aptamers bind their ligands in overlapping positions, while the guanidine binds higher within the stem. The G96A point mutation (aqua, arrow) switches ligand specificity from PRPP to ppGpp. (C) Chemical structures of the ligands bound by the ykkC subtype 1, 2a, and 2b riboswitches.