ArticleNature2013
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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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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Who cites it
103 citing papers in PubMed, 150 citations in OpenAlex.
- Molecular insights into dynamic RNA quaternary assemblies.RNA biology · 2026Review
- Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation.Research square · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- tRNA-dependent conformational dynamics and folding coordinate translational regulation by a full-length T-box riboswitch.Nature communications · 2025Article
- Structural insights into higher-order natural RNA-only multimers.Nature structural & molecular biology · 2025Article
- Crystal structures of free-state tRNARNA (New York, N.Y.) · 2025Article
- Targeting Gene Transcription Prevents Antibiotic Resistance.Antibiotics (Basel, Switzerland) · 2025Review
- Structural basis of MALAT1 RNA maturation and mascRNA biogenesis.Nature structural & molecular biology · 2024Article
- Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.RNA (New York, N.Y.) · 2024Article
- Translational T-box riboswitches bind tRNA by modulating conformational flexibility.Nature communications · 2024Article
- RNA cis-regulators are important for Streptococcus pneumoniae in vivo success.PLoS genetics · 2024Article
- Recognition of the tRNA structure: Everything everywhere but not all at once.Cell chemical biology · 2024Review
- Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch.Nature communications · 2023Article
- Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.Nature communications · 2023Article
- Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions.Journal of molecular biology · 2023Article
- General Strategies for RNA X-ray Crystallography.Molecules (Basel, Switzerland) · 2023Review
- Article
- Probing RNA Structures and Interactions Using Fluorescence Lifetime Analyses.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Riboswitch-Driven Era of New Antibacterials.Antibiotics (Basel, Switzerland) · 2022Review
- Streptococcus suis TrpX is part of a tryptophan uptake system, and its expression is regulated by a T-box regulatory element.Scientific reports · 2022Article
43 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
In Gram-positive bacteria, T-box riboswitches regulate the expression of aminoacyl-tRNA synthetases and other proteins in response to fluctuating transfer RNA aminoacylation levels under various nutritional states. T-boxes reside in the 5'-untranslated regions of the messenger RNAs they regulate, and consist of two conserved domains. Stem I contains the specifier trinucleotide that base pairs with the anticodon of cognate tRNA. 3' to stem I is the antiterminator domain, which base pairs with the tRNA acceptor end and evaluates its aminoacylation state. Despite high phylogenetic conservation and widespread occurrence in pathogens, the structural basis of tRNA recognition by this riboswitch remains ill defined. Here we demonstrate that the ~100-nucleotide T-box stem I is necessary and sufficient for specific, high-affinity (dissociation constant (Kd) ~150 nM) tRNA binding, and report the structure of Oceanobacillus iheyensis glyQ stem I in complex with its cognate tRNA at 3.2 Å resolution. Stem I recognizes the overall architecture of tRNA in addition to its anticodon, something accomplished by large ribonucleoproteins such as the ribosome, or proteins such as aminoacyl-tRNA synthetases, but is unprecedented for a compact mRNA domain. The C-shaped stem I cradles the L-shaped tRNA, forming an extended (1,604 Å(2)) intermolecular interface. In addition to the specifier-anticodon interaction, two interdigitated T-loops near the apex of stem I stack on the tRNA elbow in a manner analogous to those of the J11/12-J12/11 motif of RNase P and the L1 stalk of the ribosomal E-site. Because these ribonucleoproteins and T-boxes are unrelated, this strategy to recognize a universal tRNA feature probably evolved convergently. Mutually induced fit of stem I and the tRNA exploiting the intrinsic flexibility of tRNA and its conserved post-transcriptional modifications results in high shape complementarity, which in addition to providing specificity and affinity, globally organizes the T-box to orchestrate tRNA-dependent transcription regulation.
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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.