Download MendeleyStructure-based principles underlying ligand recognition of xanthine-II riboswitch.
Xu, X., He, M., Tai, X., Ren, Q., Shen, X., Li, C., Ren, A.(2025) Sci China Life Sci
- PubMed: 40304919
- DOI: https://doi.org/10.1007/s11427-024-2800-0
- Primary Citation of Related Structures:
9IWF, 9IWG - PubMed Abstract:
Riboswitches are conserved RNA elements that specifically recognize the cognate metabolites and regulate downstream gene expression involved in the metabolic pathways. To date, two classes of xanthine-responsive riboswitches involved in xanthine homeostasis have been identified. The recently reported xanthine-II riboswitch originates from guanine riboswitch family, featuring a single U-to-G mutation and several nucleotide insertions. Here, we report the complex structure of xanthine-II riboswitch bound to xanthine. The tertiary structure of xanthine-II riboswitch adopts a three-way junction scaffold similar to that of guanine riboswitch. However, the distinctive mutation and insertions in xanthine-II riboswitch facilitate the formation of a highly specific binding pocket for xanthine, distinguishing it from guanine riboswitches. Xanthine is bound in the junction region, forming a base triple with C64 and the mutant nucleotide G37, and is sandwiched by one base pair U8-A38 and one base triple A7-C36-U65. Structural alignment and ligand recognition specificity of the xanthine-II riboswitch are further verified by ligand-binding assays of structure-based mutation using isothermal titration calorimetry. Furthermore, leveraging the ligand specificity of the xanthine-II riboswitch, we develop a highly specific and sensitive biosensor for xanthine detection by fusing xanthine-II riboswitch with Pepper fluorogenic aptamer, highlighting the potential applications of xanthine-II riboswitch in diagnosing diseases related to xanthine metabolism disorders.
Organizational Affiliation:
Department of Cardiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
