ArticleThe Journal of biological chemistry2009
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
Article in The Journal of biological chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
54 citing papers in PubMed, 73 citations in OpenAlex.
- The S180R Human Germline Variant of DNA Polymerase β Is a Low Fidelity Enzyme with Reduced Flexibility of the Fingers Domain.Biochemistry · 2026Article
- Base excision repair in chromatin: A tug-of-war for DNA damage.DNA repair · 2025Review
- Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions.Nature communications · 2025Article
- Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β.Nature communications · 2025Article
- Unveiling the Mechanism of Deprotonation and Proton Transfer of DNA Polymerase Catalysis via Single-Molecule Conductance.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Error-Prone DNA Synthesis on Click-Ligated Templates.Doklady. Biochemistry and biophysics · 2024Article
- Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides.International journal of molecular sciences · 2024Article
- Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA PolymeraseInternational journal of molecular sciences · 2023Article
- Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes.International journal of molecular sciences · 2022Article
- Interlocking activities of DNA polymerase β in the base excision repair pathway.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Phosphorylation Induced Conformational Transitions in DNA PolymeraseFrontiers in molecular biosciences · 2022Article
- History of DNA polymerase β X-ray crystallography.DNA repair · 2020Review
- DNA polymerase β: Closing the gap between structure and function.DNA repair · 2020Review
- Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion.The Biochemical journal · 2020Article
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- DNA polymerase β nucleotide-stabilized template misalignment fidelity depends on local sequence context.The Journal of biological chemistry · 2020Article
- I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.Nucleic acids research · 2018Article
- Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair.DNA repair · 2018Review
- The nature of the DNA substrate influences pre-catalytic conformational changes of DNA polymerase β.The Journal of biological chemistry · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Apurinic/apyrimidinic (AP) sites are continuously generated in genomic DNA. Left unrepaired, AP sites represent noninstructional premutagenic lesions that are impediments to DNA synthesis. When DNA polymerases encounter an AP site, they generally insert dAMP. This preferential insertion is referred to as the A-rule. Crystallographic structures of DNA polymerase (pol) beta, a family X polymerase, with active site mismatched nascent base pairs indicate that the templating (i.e. coding) base is repositioned outside of the template binding pocket thereby diminishing interactions with the incorrect incoming nucleotide. This effectively produces an abasic site because the template pocket is devoid of an instructional base. However, the template pocket is not empty; an arginine residue (Arg-283) occupies the space vacated by the templating nucleotide. In this study, we analyze the kinetics of pol beta insertion opposite an AP site and show that the preferential incorporation of dAMP is lost with the R283A mutant. The crystallographic structures of pol beta bound to gapped DNA with an AP site analog (tertrahydrofuran) in the gap (binary complex) and with an incoming nonhydrolyzable dATP analog (ternary complex) were solved. These structures reveal that binding of the dATP analog induces a closed polymerase conformation, an unstable primer terminus, and an upstream shift of the templating residue even in the absence of a template base. Thus, dATP insertion opposite an abasic site and dATP misinsertions have common features.
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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.