The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg²⁺-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution.

细菌核糖开关的ykkC家族结合了几种广泛的类别，这些类别具有相似的二级结构和共有基序，但响应不同的细胞代谢产物而控制不同的基因。在这里，我们报告了两个独特的ykkC核糖开关的晶体结构，它们分别与它们的同源配体ppGpp（参与应激反应的第二个信使）或PRPP（嘌呤生物合成的前体）特异性结合。两种RNA都采用相似的结构，并包含一个以前在胍基特异性ykkC核糖开关中观察到的保守核心。但是，ppGpp和PRPP核糖开关独特地采用了一个附加的螺旋元件，该螺旋元件连接配体感应域的末端，并为直接和Mg ²⁺建立了隧道。介导的配体结合。突变和足迹实验凸显了形成通道和长距离接触的保守核苷酸对于配体结合和遗传反应的重要性。我们的工作为核糖开关的特异性提供了新的见解，并为以后的RNA进化研究提供了独特的机会。