ArticleNucleic acids research2023
Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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27 citing papers in PubMed.
- DNA polymerase I and DnaE mediate RNA-templated DNA synthesis over embedded ribonucleotides.Nucleic acids research · 2026Article
- Structural and single-molecule insights into the core human mitochondrial DNA replisome.The Biochemical journal · 2026Review
- Recombinant Thermostable DNA Polymerases: Current Approaches to Production, Molecular Engineering, and Applications in Biotechnology and Diagnostics.International journal of molecular sciences · 2026Review
- Translesion DNA synthesis on pyrimidine dimers by plant organellar DNA polymerases is metal-dependent.Nucleic acids research · 2026Article
- DNA polymerase I: structure, activity, and function in bacterial DNA replication and repair.Critical reviews in biochemistry and molecular biology · 2026Review
- Bst DNA Polymerase: Structure, Properties and Engineering Strategies in LAMP.International journal of molecular sciences · 2026Review
- Diversity and distribution of bacterial DNA polymerases.Nucleic acids research · 2026Article
- Functional convergence in Z-DNA biosynthesis highlighted by the characterization of nucleotide metabolism enzymes in bacteriophages.Nucleic acids research · 2026Article
- Diversity ofInternational journal of molecular sciences · 2026Article
- Diverse bacterial pattern recognition receptors sense the conserved phage proteome.bioRxiv : the preprint server for biology · 2026Article
- DNA polymerase I is an efficient reverse transcriptase that mediates RNA-templated DNA repair synthesis.bioRxiv : the preprint server for biology · 2025Article
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- CRISPR-DNA Polymerase Assisted Targeted Mutagenesis for Regulable Laboratory Evolution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.Nucleic acids research · 2025Article
- Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair.Nucleic acids research · 2025Article
- Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase.Nature communications · 2025Article
- Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes.Molecular biology and evolution · 2025Article
- The evolutionarily diverged single-stranded DNA-binding proteins SSB1/SSB2 differentially affect the replication, recombination and mutation of organellar genomes inPlant diversity · 2025Article
- Cryo-EM Structures of the Plasmodium falciparum Apicoplast DNA Polymerase.Journal of molecular biology · 2024Article
- DNA polymerase swapping in Caudoviricetes bacteriophages.Virology journal · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3'-5' exo and pol domains into two separate genes, observed in PolAs for the first time.
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