ArticleProceedings of the National Academy of Sciences of the United States of America2012
Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 56 citations in OpenAlex.
- Comprehensive Analysis of Insertions in BVDV and Implications for Non-Homologous Recombination Mechanisms.Viruses · 2026Article
- Enzymology of the metazoan tRNA ligase complex: a lifetime in cycles.Cellular and molecular life sciences : CMLS · 2026Review
- Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation.Nature structural & molecular biology · 2025Article
- Structural and biochemical characterization of the 3'-5' tRNA splicing ligases.The Journal of biological chemistry · 2025Article
- DDX1 is required for non-spliceosomal splicing of tRNAs but not of XBP1 mRNA.Communications biology · 2025Article
- Fungi of the order Mucorales express a "sealing-only" tRNA ligase.RNA (New York, N.Y.) · 2024Article
- Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.Nature communications · 2024Article
- Recognition of the tRNA structure: Everything everywhere but not all at once.Cell chemical biology · 2024Review
- Fungi of the order Mucorales express a "sealing-only" tRNA ligase.bioRxiv : the preprint server for biology · 2023Article
- Insights into the structure and function of the RNA ligase RtcB.Cellular and molecular life sciences : CMLS · 2023Review
- The life and times of a tRNA.RNA (New York, N.Y.) · 2023Review
- Structures of RNA ligase RtcB in complexes with divalent cations and GTP.RNA (New York, N.Y.) · 2022Article
- Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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- The expanding field of non-canonical RNA capping: new enzymes and mechanisms.Royal Society open science · 2021Review
- Ligation of 2', 3'-cyclic phosphate RNAs for the identification of microRNA binding sites.FEBS letters · 2021Article
- Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.Nucleic acids research · 2019Article
- Structure and two-metal mechanism of fungal tRNA ligase.Nucleic acids research · 2019Article
- The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity.Nucleic acids research · 2018Article
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
The RtcB protein has recently been identified as a 3'-phosphate RNA ligase that directly joins an RNA strand ending with a 2',3'-cyclic phosphate to the 5'-hydroxyl group of another RNA strand in a GTP/Mn(2+)-dependent reaction. Here, we report two crystal structures of Pyrococcus horikoshii RNA-splicing ligase RtcB in complex with Mn(2+) alone (RtcB/ Mn(2+)) and together with a covalently bound GMP (RtcB-GMP/Mn(2+)). The RtcB/ Mn(2+) structure (at 1.6 Å resolution) shows two Mn(2+) ions at the active site, and an array of sulfate ions nearby that indicate the binding sites of the RNA phosphate backbone. The structure of the RtcB-GMP/Mn(2+) complex (at 2.3 Å resolution) reveals the detailed geometry of guanylylation of histidine 404. The critical roles of the key residues involved in the binding of the two Mn(2+) ions, the four sulfates, and GMP are validated in extensive mutagenesis and biochemical experiments, which also provide a thorough characterization for the three steps of the RtcB ligation pathway: (i) guanylylation of the enzyme, (ii) guanylyl-transfer to the RNA substrate, and (iii) overall ligation. These results demonstrate that the enzyme's substrate-induced GTP binding site and the putative reactive RNA ends are in the vicinity of the binuclear Mn(2+) active center, which provides detailed insight into how the enzyme-bound GMP is tansferred to the 3'-phosphate of the RNA substrate for activation and subsequent nucleophilic attack by the 5'-hydroxyl of the second RNA substrate, resulting in the ligated product and release of GMP.
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