ArticleRNA biology2014
A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications.
Article in RNA biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
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- A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.Nucleic acids research · 2024Article
- Decoding the ribosome's hidden language: rRNA modifications as key players in cancer dynamics and targeted therapies.Clinical and translational medicine · 2024Review
- New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts.NAR genomics and bioinformatics · 2023Article
- Ribosome-associated quality-control mechanisms from bacteria to humans.Molecular cell · 2022Review
- Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing.Molecular cell · 2021Article
- Ribosome Rescue Pathways in Bacteria.Frontiers in microbiology · 2021Review
- Detection and Degradation of Stalled Nascent Chains via Ribosome-Associated Quality Control.Annual review of biochemistry · 2020Review
- PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model DiatomFrontiers in plant science · 2020Article
- Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives.The Journal of biological chemistry · 2019Article
- Article
- The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways.International journal of molecular sciences · 2019Review
- The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications.Biology direct · 2015Article
- Structure and assembly pathway of the ribosome quality control complex.Molecular cell · 2015Article
- Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.Science (New York, N.Y.) · 2015Article
- Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Resilience of biochemical activity in protein domains in the face of structural divergence.Current opinion in structural biology · 2014Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A protein family including mammalian NEMF, Drosophila caliban, yeast Tae2, and bacterial FpbA-like proteins was first defined over a decade ago and found to be universally distributed across the three domains/superkingdoms of life. Since its initial characterization, this family of proteins has been tantalizingly linked to a wide range of biochemical functions. Tapping the enormous wealth of genome information that has accumulated since the initial characterization of these proteins, we perform a detailed computational analysis of the family, identifying multiple conserved domains. Domains identified include an enzymatic domain related to the formamidopyrimidine (Fpg), MutM, and Nei/EndoVIII family of DNA glycosylases, a novel, predicted RNA-binding domain, and a domain potentially mediating protein-protein interactions. Through this characterization, we predict that the DNA glycosylase-like domain catalytically operates on double-stranded RNA, as part of a hitherto unknown base modification mechanism that probably targets rRNAs. At least in archaea, and possibly eukaryotes, this pathway might additionally include the AMMECR1 family of proteins. The predicted RNA-binding domain associated with this family is also observed in distinct architectural contexts in other proteins across phylogenetically diverse prokaryotes. Here it is predicted to play a key role in a new pathway for tRNA 4-thiouridylation along with TusA-like sulfur transfer proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.