ArticleBiochemistry2011
Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 46 citations in OpenAlex.
- Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis.Molecular cell · 2026Article
- The proofreading mechanism of the human leading-strand DNA polymerase ε holoenzyme.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.Nature communications · 2023Article
- Cryo-EM structures of human monkeypox viral replication complexes with and without DNA duplex.Cell research · 2023Article
- Structural Insights into Binding of Remdesivir Triphosphate within the Replication-Transcription Complex of SARS-CoV-2.Biochemistry · 2022Article
- On the damage done to the structure of the Thermoplasma acidophilum proteasome by electron radiation.Protein science : a publication of the Protein Society · 2018Article
- I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.Nucleic acids research · 2018Article
- Fidelity of DNA replication-a matter of proofreading.Current genetics · 2018Review
- On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.Protein science : a publication of the Protein Society · 2017Article
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- Modulation of DNA Polymerase Noncovalent Kinetic Transitions by Divalent Cations.The Journal of biological chemistry · 2016Article
- Article
- Switching between polymerase and exonuclease sites in DNA polymerase ε.Nucleic acids research · 2015Article
- Kinetic mechanisms governing stable ribonucleotide incorporation in individual DNA polymerase complexes.Biochemistry · 2014Article
- RB69 DNA polymerase structure, kinetics, and fidelity.Biochemistry · 2014Review
- Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.Protein science : a publication of the Protein Society · 2014Article
- Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site.Chemical reviews · 2014Review
- Dynamics of translocation and substrate binding in individual complexes formed with active site mutants of {phi}29 DNA polymerase.The Journal of biological chemistry · 2014Article
- Structural basis for processive DNA synthesis by yeast DNA polymerase ɛ.Nature structural & molecular biology · 2014Article
- Engineering processive DNA polymerases with maximum benefit at minimum cost.Frontiers in microbiology · 2014Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Bacteriophage RB69 DNA polymerase (RB69 pol) has served as a model for investigating how B family polymerases achieve a high level of fidelity during DNA replication. We report here the structure of an RB69 pol ternary complex at 1.8 Å resolution, extending the resolution from our previously reported structure at 2.6 Å [Franklin, M. C., et al. (2001) Cell 105, 657-667]. In the structure presented here, a network of five highly ordered, buried water molecules can be seen to interact with the N3 and O2 atoms in the minor groove of the DNA duplex. This structure reveals how the formation of the closed ternary complex eliminates two ordered water molecules, which are responsible for a kink in helix P in the apo structure. In addition, three pairs of polar-nonpolar interactions have been observed between (i) the Cα hydrogen of G568 and the N3 atom of the dG templating base, (ii) the O5' and C5 atoms of the incoming dCTP, and (iii) the OH group of S565 and the aromatic face of the dG templating base. These interactions are optimized in the dehydrated environment that envelops Watson-Crick nascent base pairs and serve to enhance base selectivity in wild-type RB69 pol.
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