ArticleNature structural & molecular biology2009
Structural basis of ligand binding by a c-di-GMP riboswitch.
Article in Nature structural & molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
174 citing papers in PubMed, 284 citations in OpenAlex.
- A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM.Nucleic acids research · 2026Article
- Cryo-EM structures reveal a conserved architecture for raiA noncoding RNA.Nucleic acids research · 2026Article
- Parallel regulatory circuits orchestrate biofilm formation in response to c-di-GMP levels and growth phase.PLoS genetics · 2025Article
- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (New York, N.Y.) · 2024Article
- Mechanism of Dual-Site Recognition in a Classic DNA Aptamer.Journal of chemical information and modeling · 2024Article
- Riboswitch Mechanisms for Regulation of P1 Helix Stability.International journal of molecular sciences · 2024Review
- Article
- Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform fromMicrobiology spectrum · 2024Article
- Development of Allosteric Ribozymes for ATP and l-Histidine Based on the R3C Ligase Ribozyme.Life (Basel, Switzerland) · 2024Article
- The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches.Biochemistry · 2024Article
- Origin of ribonucleotide recognition motifs through ligand mimicry at early earth.RNA biology · 2024Review
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- One-Flask Synthesis of Cyclic Diguanosine Monophosphate (c-di-GMP).Current protocols · 2023Article
- General Strategies for RNA X-ray Crystallography.Molecules (Basel, Switzerland) · 2023Review
- Recent advances and perspectives in nucleotide second messenger signaling in bacteria.microLife · 2023Review
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Riboswitch-Driven Era of New Antibacterials.Antibiotics (Basel, Switzerland) · 2022Review
- Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets.Antibiotics (Basel, Switzerland) · 2022Article
- Dynamics of metal binding and mutation in yybP-ykoY riboswitch ofRSC advances · 2022Article
114 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
The second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 A resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP signaling.
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Registered trials
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.