ArticleNucleic acids research2013
Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.
Article in Nucleic acids research, 2013. 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.
- Identification of fidelity-determined residues of Porcine reproductive and respiratory syndrome virus through structural alignment.Virulence · 2026Article
- Revealing deep evolutionary relationships between RNA viruses using predicted structural models of viral RNA polymerases.Molecular biology and evolution · 2026Article
- Unveiling the RNA virus landscape ofVirus evolution · 2026Article
- Structural characterization of the full-length Hantaan virus polymerase.PLoS pathogens · 2024Article
- Fidelity Characterization of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and NADC30-like Strain.Viruses · 2024Article
- Molecular characterization of a novel ambiguivirus isolated from the phytopathogenic fungus Setosphaeria turcica.Archives of virology · 2023Article
- Preparing for the next viral threat with broad-spectrum antivirals.The Journal of clinical investigation · 2023Review
- Template Entrance Channel as Possible Allosteric Inhibition and Resistance Site for Quinolines Tricyclic Derivatives in RNA Dependent RNA Polymerase of Bovine Viral Diarrhea Virus.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies.Viruses · 2022Review
- Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited.Journal of molecular evolution · 2022Article
- Structural insights into RNA polymerases of negative-sense RNA viruses.Nature reviews. Microbiology · 2021Review
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- Rational Control of Poliovirus RNA-Dependent RNA Polymerase Fidelity by Modulating Motif-D Loop Conformational Dynamics.Biochemistry · 2019Article
- Transcriptional Control and mRNA Capping by the GDP Polyribonucleotidyltransferase Domain of the Rabies Virus Large Protein.Viruses · 2019Review
- RNA Synthesis and Capping by Non-segmented Negative Strand RNA Viral Polymerases: Lessons From a Prototypic Virus.Frontiers in microbiology · 2019Review
- Calicivirus RNA-Dependent RNA Polymerases: Evolution, Structure, Protein Dynamics, and Function.Frontiers in microbiology · 2019Review
- Review
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- Homology-Based Identification of a Mutation in the Coronavirus RNA-Dependent RNA Polymerase That Confers Resistance to Multiple Mutagens.Journal of virology · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-dependent RNA polymerase (RdRp) is essential to viral replication and is therefore one of the primary targets of countermeasures against these dangerous infectious agents. Development of broad-spectrum therapeutics targeting polymerases has been hampered by the extreme sequence variability of these sequences. RdRps range in length from 400-800 residues, yet contain only ∼20 residues that are conserved in most species. In this study, we made structure-based comparisons that are independent of sequence composition using a recently developed algorithm. We identified residue-to-residue correspondences of multiple protein structures and created (two-dimensional) structure-based alignment maps of 37 polymerase structures that provide both sequence and structure details. Using these maps, we determined that ∼75% of each polymerase species consists of seven protein segments, each of which has high structural similarity to segments in other species, though they are widely divergent in sequence composition and order. We define each of these segments as a 'homomorph', and each includes (though most are much larger than) the well-known conserved polymerase motifs. All homomorphs contact the template tunnel or nucleoside triphosphate (NTP) entry tunnel and the exterior of the protein, suggesting they constitute a structural and functional skeleton common among the polymerases.
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