ArticleNucleic acids research2011
Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 64 citations in OpenAlex.
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- Deep learning in the discovery of antiviral peptides and peptidomimetics: databases and prediction tools.Molecular diversity · 2025Review
- Mechanisms of ribosomopathy and phase separation-related ribosomopathy.Journal of Zhejiang University. Science. B · 2025Review
- Structural insight into the novel Thermus thermophilus SPOUT methyltransferase RlmR catalysing Um2552 formation in the 23S rRNA A-loop: a case of convergent evolution.Nucleic acids research · 2025Article
- tRNA mbioRxiv : the preprint server for biology · 2023Article
- Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.Computational and structural biotechnology journal · 2023Article
- Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases.The Journal of biological chemistry · 2022Review
- Mutations in RPS19 may affect ribosome function and biogenesis in Diamond Blackfan anemia.FEBS open bio · 2022Article
- Increased expression of NOP14 is associated with improved prognosis due to immune regulation in colorectal cancer.BMC gastroenterology · 2022Article
- The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase binding in 40S ribosome assembly.RNA (New York, N.Y.) · 2022Article
- Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat.BMC genomics · 2021Article
- Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.PLoS computational biology · 2020Article
- Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors.The Plant cell · 2019Review
- A Family Divided: Distinct Structural and Mechanistic Features of the SpoU-TrmD (SPOUT) Methyltransferase Superfamily.Biochemistry · 2019Article
- Ribosome assembly coming into focus.Nature reviews. Molecular cell biology · 2019Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen-Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase.
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