ArticleThe Journal of biological chemistry2015
Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5'-end-dependent mRNA decay.
Article in The Journal of biological chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- 5'-terminal glycosylation of protein-coding transcripts: An epitranscriptomic modification that prolongs mRNA lifetimes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.Nature communications · 2024Article
- Visualization of mutagenic nucleotide processing byProceedings of the National Academy of Sciences of the United States of America · 2022Article
- A distinct RNA recognition mechanism governs NpProceedings of the National Academy of Sciences of the United States of America · 2022Article
- NUDT2 initiates viral RNA degradation by removal of 5'-phosphates.Nature communications · 2021Article
- Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.Nucleic acids research · 2020Article
- Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inRNA (New York, N.Y.) · 2020Article
- YvcI fromThe Journal of biological chemistry · 2019Article
- TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs.Nucleic acids research · 2019Article
- Noncanonical features and modifications on the 5'-end of bacterial sRNAs and mRNAs.Wiley interdisciplinary reviews. RNA · 2019Review
- mRNA decapping: finding the right structures.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.Nucleic acids research · 2018Article
- Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.Nucleic acids research · 2018Article
- Article
- A Novel RNA Phosphorylation State Enables 5' End-Dependent Degradation in Escherichia coli.Molecular cell · 2017Article
- Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets.The Journal of biological chemistry · 2017Article
- Article
- Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to mNature structural & molecular biology · 2016Article
- Structure and function of the bacterial decapping enzyme NudC.Nature chemical biology · 2016Article
- Distinct Requirements for 5'-Monophosphate-assisted RNA Cleavage by Escherichia coli RNase E and RNase G.The Journal of biological chemistry · 2016Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation pathway by removing pyrophosphate from the triphosphorylated RNA 5' terminus. Here, we report the x-ray structures of Escherichia coli RppH (EcRppH) in apo- and RNA-bound forms. These structures show distinct conformations of EcRppH·RNA complexes on the catalytic pathway and suggest a common catalytic mechanism for Nudix hydrolases. EcRppH interacts with RNA by a bipartite mechanism involving specific recognition of the 5'-terminal triphosphate and the second nucleotide, thus enabling discrimination against mononucleotides as substrates. The structures also reveal the molecular basis for the preference of the enzyme for RNA substrates bearing guanine in the second position by identifying a protein cleft in which guanine interacts with EcRppH side chains via cation-π contacts and hydrogen bonds. These interactions explain the modest specificity of EcRppH at the 5' terminus and distinguish the enzyme from the highly selective RppH present in Bacillus subtilis. The divergent means by which RNA is recognized by these two functionally and structurally analogous enzymes have important implications for mRNA decay and the regulation of protein biosynthesis in bacteria.
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