ArticleStructure (London, England : 1993)2015
The Closing Mechanism of DNA Polymerase I at Atomic Resolution.
Article in Structure (London, England : 1993), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- A Thymine Dimer Stalls a High-Fidelity DNA Polymerase by Providing No Template Information in the Same Manner as an Abasic Site.Biochemistry · 2026Article
- Single-residue engineering of Klenow fragment enables broad acceptance of chemically modified nucleotides.Nucleic acids research · 2026Article
- Bst DNA Polymerase: Structure, Properties and Engineering Strategies in LAMP.International journal of molecular sciences · 2026Review
- Understanding the Fidelity and Specificity of DNA Polymerase I.ACS omega · 2025Article
- Comparing Force Field Treatments in QM/MM Studies of the SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) Mechanism.Journal of chemical theory and computation · 2025Article
- Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.Nucleic acids research · 2025Article
- Structural basis for substrate binding and selection by human mitochondrial RNA polymerase.Nature communications · 2024Article
- Melanoma-Derived DNA Polymerase Theta Variants Exhibit Altered DNA Polymerase Activity.Biochemistry · 2024Article
- A four-point molecular handover during Okazaki maturation.Nature structural & molecular biology · 2023Article
- Single-molecule Taq DNA polymerase dynamics.Science advances · 2022Article
- Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8.Nucleic acids research · 2021Article
- Review
- Biflavonoid-Induced Disruption of Hydrogen Bonds Leads to Amyloid-β Disaggregation.International journal of molecular sciences · 2021Article
- Building better polymerases: Engineering the replication of expanded genetic alphabets.The Journal of biological chemistry · 2020Review
- Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.Nucleic acids research · 2020Article
- Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase.Journal of the American Chemical Society · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Insights into DNA polymerase δ's mechanism for accurate DNA replication.Journal of molecular modeling · 2019Article
- I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.Nucleic acids research · 2018Article
- Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.eLife · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase I bound to DNA in the open conformation with a dNTP present in the active site. We use this structure to computationally simulate the open to closed transition of DNA polymerase in the presence of a Watson-Crick base pair. Our microsecond simulations allowed us to characterize the key steps involved in active site assembly, and propose the sequence of events involved in the prechemistry steps of DNA polymerase catalysis. They also reveal new features of the polymerase mechanism, such as a conserved histidine as a potential proton acceptor from the primer 3'-hydroxyl.
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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.