ArticleNucleic acids research2021
Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- High-throughput Screening of Sequence Elements Associated with RNA Localization.Computational and structural biotechnology journal · 2026Article
- Integration of the hammerhead ribozyme into structured RNAs to measure ligand-binding events for riboswitch candidates and aptamers.Acta biochimica et biophysica Sinica · 2025Article
- Tiny but multi-stable: four distinct conformational states govern the ligand-free state of the preQ1 riboswitch from a thermophilic bacterium.Nucleic acids research · 2025Article
- Engineering oxypurinol-responsive riboswitches based on bacterial xanthine aptamers for gene expression control in mammalian cell culture.Nucleic acids research · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.Biophysical journal · 2024Article
- Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch.Nature communications · 2023Article
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Mechanism of Ligand Discrimination by theJournal of chemical information and modeling · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Structural insights into translation regulation by the THF-II riboswitch.Nucleic acids research · 2023Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structure and mechanism of the methyltransferase ribozyme MTR1.Nature chemical biology · 2022Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.