ArticleRNA (New York, N.Y.)2018
Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches.
Article in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and Short Hydrogen Bonds in Biomacromolecular Complexes.Angewandte Chemie (International ed. in English) · 2025Article
- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches.Biochemistry · 2024Article
- Structure and mechanism of the methyltransferase ribozyme MTR1.Nature chemical biology · 2022Article
- AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation.Nucleic acids research · 2021Article
- NMR characterization of RNA small molecule interactions.Methods (San Diego, Calif.) · 2019Review
- The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry.Nucleic acids research · 2019Article
- Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function.ACS omega · 2019Article
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4 authors at 1 institution in 1 country.
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Abstract
In certain structural or functional contexts, RNA structures can contain protonated nucleotides. However, a direct role for stably protonated nucleotides in ligand binding and ligand recognition has not yet been demonstrated unambiguously. Previous X-ray structures of c-GAMP binding riboswitch aptamer domains in complex with their near-cognate ligand c-di-GMP suggest that an adenine of the riboswitch either forms two hydrogen bonds to a G nucleotide of the ligand in the unusual enol tautomeric form or that the adenine in its N1 protonated form binds the G nucleotide of the ligand in its canonical keto tautomeric state. By using NMR spectroscopy we demonstrate that the c-GAMP riboswitches bind c-di-GMP using a stably protonated adenine in the ligand binding pocket. Thereby, we provide novel insights into the putative biological functions of protonated nucleotides in RNA, which in this case influence the ligand selectivity in a 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.