The widespread ykkC-I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the Burkholderia sp. TJI49 ykkC-I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from Dickeya dadantii and Sulfobacillus acidophilus, our Burkholderia structure reveals a chelated K⁺ ion adjacent to two Mg²⁺ ions in the guanidine-binding pocket. Thermal melting analysis shows that K⁺ chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K⁺(Mg²⁺)₂] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of ykkC-I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K⁺ chelation in the Burkholderia Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg²⁺ ion binding in place of the K⁺ ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among ykkC-I riboswitches.

中文翻译：

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一种罕见的 [K+(Mg2+)2] 金属离子三元组赋予胍-I 核糖开关稳定性和选择性

广泛存在的ykkC -I 核糖开关类例证了不同的核糖开关进化。为了分析自然选择如何使其多功能 RNA 折叠多样化，我们确定了伯克霍尔德氏菌的 X 射线晶体结构。TJI49 ykkC -I subtype-1（胍-I）核糖开关适体结构域。与先前报道的来自Dickeya dadantii和Sulfobacillus acidophilus的直系同源物结构不同，我们的伯克霍尔德氏菌结构揭示了与胍结合袋中的两个 Mg ²⁺离子相邻的螯合 K ^+离子。热熔分析表明，K ⁺螯合会在结合袋中诱导局部构象变化，从而改善胍-RNA相互作用。核糖体结构分析表明[K ⁺ (Mg ²⁺ ) ₂ ] 离子三联体并不常见。然而，它让人想起在核酶和 DNA 聚合酶的活性位点中发现的金属离子簇。先前对结合效应配体 ppGpp 和 PRPP 的ykkC -I subtype-2 RNA的结构表征表明，在这些旁系同源物中，负责伯克霍尔德菌胍-I 核糖开关中K ⁺螯合的腺嘌呤被嘧啶取代。这种突变导致水分子和 Mg ²⁺离子结合代替 K⁺离子。因此，我们的结构分析证明了离子和溶剂螯合如何调节ykkC -I 核糖开关之间的不同配体特异性和亲和力。