ArticleNature2009
Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.
Article in Nature, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 papers.
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Who cites it
137 citing papers in PubMed, 213 citations in OpenAlex.
- Mechanisms of transcription termination across the coding and noncoding loci of the genome.Nature reviews. Molecular cell biology · 2026Review
- Arabidopsis DXO1- and RNMT1-Mediated mPlant, cell & environment · 2026Article
- Spt5's central KOW domains and the Pol II stalk collaborate to regulate chromatin and 3'-end processing in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2026Article
- Crystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap and molecular mechanism for the decapping reactions.Nucleic acids research · 2026Article
- The Arabidopsis deNADding Enzyme DXO1 Modulates the Plant Immunity Response.Plant, cell & environment · 2026Article
- Mammalian tRNA acetylation determines translation efficiency and tRNA quality control.Nature communications · 2025Article
- Defective Processing of Cytoplasmic and Chloroplast Ribosomal RNA in the Absence of Arabidopsis DXO1.Plant, cell & environment · 2025Article
- Molecular basis for the interaction between Saccharomyces cerevisiae Rtt103 and the Rat1-Rai1 complex.Nature communications · 2025Article
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- The Mysterious World of Non-Canonical Caps - What We Know and Why We Need New Sequencing Techniques.Chembiochem : a European journal of chemical biology · 2025Review
- DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.Nature communications · 2025Article
- Transcriptome-Wide Analysis of the 5' Cap Status of RNA Using 5' Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Toward structural understanding of eukaryotic transcription elongation.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Studying Exoribonuclease Activity Using Fluorescence Anisotropy Assay.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Independent neofunctionalization of Dxo1 inRNA (New York, N.Y.) · 2024Article
- USP36 SUMOylates Las1L and Promotes Its Function in Pre-Ribosomal RNA ITS2 Processing.Cancer research communications · 2024Article
- Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex.Nature communications · 2024Article
- A Plasmodium apicoplast-targeted unique exonuclease/FEN exhibits interspecies functional differences attributable to an insertion that alters DNA-binding.Nucleic acids research · 2024Article
- The making and breaking of tRNAs by ribonucleases.Trends in genetics : TIG · 2024Review
77 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The 5'-->3' exoribonucleases (XRNs) comprise a large family of conserved enzymes in eukaryotes with crucial functions in RNA metabolism and RNA interference. XRN2, or Rat1 in yeast, functions primarily in the nucleus and also has an important role in transcription termination by RNA polymerase II (refs 7-14). Rat1 exoribonuclease activity is stimulated by the protein Rai1 (refs 15, 16). Here we report the crystal structure at 2.2 A resolution of Schizosaccharomyces pombe Rat1 in complex with Rai1, as well as the structures of Rai1 and its murine homologue Dom3Z alone at 2.0 A resolution. The structures reveal the molecular mechanism for the activation of Rat1 by Rai1 and for the exclusive exoribonuclease activity of Rat1. Biochemical studies confirm these observations, and show that Rai1 allows Rat1 to degrade RNAs with stable secondary structure more effectively. There are large differences in the active site landscape of Rat1 compared to related and PIN (PilT N terminus) domain-containing nucleases. Unexpectedly, we identified a large pocket in Rai1 and Dom3Z that contains highly conserved residues, including three acidic side chains that coordinate a divalent cation. Mutagenesis and biochemical studies demonstrate that Rai1 possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA. Such an activity is important for messenger RNA degradation in bacteria, but this is, to our knowledge, the first demonstration of this activity in eukaryotes and suggests that Rai1/Dom3Z may have additional important functions in RNA metabolism.
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