ArticleProceedings of the National Academy of Sciences of the United States of America2015
Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 32 citations in OpenAlex.
- Detection and sequencing of ApProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles.Nature structural & molecular biology · 2025Article
- Circular RNAs in Archaea.Advances in experimental medicine and biology · 2025Review
- Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Manganese(II) promotes prebiotically plausible non-enzymatic RNA ligation reactions.Chemical communications (Cambridge, England) · 2024Article
- Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation.bioRxiv : the preprint server for biology · 2024Article
- Characterization of tRNA splicing enzymes RNA ligase and tRNA 2'-phosphotransferase from the pathogenic fungi Mucorales.RNA (New York, N.Y.) · 2024Article
- Development of Thermotolerant Lactobacilli Cultures with Improved Probiotic Properties Using Adaptive Laboratory Evolution Method.Probiotics and antimicrobial proteins · 2023Article
- Chemoproteomic discovery of a human RNA ligase.Nature communications · 2023Article
- Article
- Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.Nucleic acids research · 2020Review
- Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.Nucleic acids research · 2020Article
- Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.Nucleic acids research · 2019Article
- Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.The Journal of biological chemistry · 2019Article
- Structure and two-metal mechanism of fungal tRNA ligase.Nucleic acids research · 2019Article
- Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues.Nature communications · 2019Article
- Deinococcus radiodurans HD-Pnk, a Nucleic Acid End-Healing Enzyme, Abets Resistance to Killing by Ionizing Radiation and Mitomycin C.Journal of bacteriology · 2018Article
- Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.Nature communications · 2018Article
- High-throughput sequencing reveals circular substrates for an archaeal RNA ligase.RNA biology · 2017Article
- Deletion of the rnl gene encoding a nick-sealing RNA ligase sensitizes Deinococcus radiodurans to ionizing radiation.Nucleic acids research · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
ATP-dependent RNA ligases are agents of RNA repair that join 3'-OH and 5'-PO4 RNA ends. Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sealing enzymes found in bacteria, viruses, and eukarya. Crystal structures of NgrRnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-Nζ)-AMP•Mn(2+) intermediate; ligase•ATP•(Mn(2+))2 Michaelis complex; and ligase•Mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound "catalytic" metal coordination complex lowers the pKa of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; and (ii) a second metal coordination complex bridges the β- and γ-phosphates. The NgrRnl N domain is a distinctively embellished oligonucleotide-binding (OB) fold that engages the γ-phosphate and associated metal complex and orients the pyrophosphate leaving group for in-line catalysis with stereochemical inversion at the AMP phosphate. The unique domain architecture of NgrRnl fortifies the theme that RNA ligases have evolved many times, and independently, by fusions of a shared nucleotidyltransferase domain to structurally diverse flanking modules. The mechanistic insights to lysine adenylylation gained from the NgrRnl structures are likely to apply broadly to the covalent nucleotidyltransferase superfamily of RNA ligases, DNA ligases, and RNA capping enzymes.
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