ArticleNucleic acids research2007
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 39 citations in OpenAlex.
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- 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
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- Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.Frontiers in molecular biosciences · 2021Review
- β-Strand-mediated interactions of protein domains.Proteins · 2020Article
- Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems.Nucleic acids research · 2020Review
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- 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
- Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases.RNA (New York, N.Y.) · 2017Article
- RNA damage in biological conflicts and the diversity of responding RNA repair systems.Nucleic acids research · 2016Review
- Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- 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
- Resilience of biochemical activity in protein domains in the face of structural divergence.Current opinion in structural biology · 2014Review
- Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding.PloS one · 2014Article
- A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications.RNA biology · 2014Article
- The enigmatic ERH protein: its role in cell cycle, RNA splicing and cancer.Protein & cell · 2013Review
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Using sensitive structure similarity searches, we identify a shared alpha+beta fold, RAGNYA, principally involved in nucleic acid, nucleotide or peptide interactions in a diverse group of proteins. These include the Ribosomal proteins L3 and L1, ATP-grasp modules, the GYF domain, DNA-recombination proteins of the NinB family from caudate bacteriophages, the C-terminal DNA-interacting domain of the Y-family DNA polymerases, the uncharacterized enzyme AMMECR1, the siRNA silencing repressor of tombusviruses, tRNA Wybutosine biosynthesis enzyme Tyw3p, DNA/RNA ligases and related nucleotidyltransferases and the Enhancer of rudimentary proteins. This fold exhibits three distinct circularly permuted versions and is composed of an internal repeat of a unit with two-strands and a helix. We show that despite considerable structural diversity in the fold, its representatives show a common mode of nucleic acid or nucleotide interaction via the exposed face of the sheet. Using this information and sensitive profile-based sequence searches: (1) we predict the active site, and mode of substrate interaction of the Wybutosine biosynthesis enzyme, Tyw3p, and a potential catalytic role for AMMECR1. (2) We provide insights regarding the mode of nucleic acid interaction of the NinB proteins, and the evolution of the active site of classical ATP-grasp enzymes and DNA/RNA ligases. (3) We also present evidence for a bacterial origin of the GYF domain and propose how this version of the fold might have been utilized in peptide interactions in the context of nucleoprotein complexes.
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Registered trials
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.