ArticleNucleic acids research2020
AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- A dynamic search mechanism enables APE1 to identify AP-sites in DNA.Nucleic acids research · 2026Article
- Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher.Nucleic acids research · 2026Article
- The PA2803-encoded PcrP exhibits a novel non-catalytic function and contributes to polymyxin B resistance inJournal of bacteriology · 2025Article
- From DNA Repair to Redox Signaling: The Multifaceted Role of APEX1 (Apurinic/Apyrimidinic Endonuclease 1) in Cardiovascular Health and Disease.International journal of molecular sciences · 2025Review
- Position-Dependent Effects of AP Sites Within anInternational journal of molecular sciences · 2025Article
- Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope.Nature methods · 2025Article
- Modelling protein-protein interactions for the design of vaccine chimeric antigens with protective epitopes.PloS one · 2025Article
- Nucleolytic processing of abasic sites underlies PARP inhibitor hypersensitivity in ALC1-deficient BRCA mutant cancer cells.Nature communications · 2024Article
- Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics.Nucleic acids research · 2023Article
- Article
- Second Harmonic Generation Interrogation of the Endonuclease APE1 Binding Interaction with G-Quadruplex DNA.Analytical chemistry · 2022Article
- Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair.ACS chemical biology · 2022Article
- Structural basis for APE1 processing DNA damage in the nucleosome.Nature communications · 2022Article
- Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1.Nature communications · 2022Article
- The contribution of PARP1, PARP2 and poly(ADP-ribosyl)ation to base excision repair in the nucleosomal context.Scientific reports · 2021Article
- APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.Nature communications · 2021Article
- Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.Computational and structural biotechnology journal · 2021Article
- Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level.Computational and structural biotechnology journal · 2021Review
- Understanding APE1 cellular functions by the structural preference of exonuclease activities.Computational and structural biotechnology journal · 2021Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
Base excision repair (BER) maintains genomic stability through the repair of DNA damage. Within BER, AP-endonuclease 1 (APE1) is a multifunctional enzyme that processes DNA intermediates through its backbone cleavage activity. To accomplish these repair activities, APE1 must recognize and accommodate several diverse DNA substrates. This is hypothesized to occur through a DNA sculpting mechanism where structural adjustments of the DNA substrate are imposed by the protein; however, how APE1 uniquely sculpts each substrate within a single rigid active site remains unclear. Here, we utilize structural and biochemical approaches to probe the DNA sculpting mechanism of APE1, specifically by characterizing a protein loop that intercalates the minor groove of the DNA (termed the intercalating loop). Pre-steady-state kinetics reveal a tyrosine residue within the intercalating loop (Y269) that is critical for AP-endonuclease activity. Using X-ray crystallography and molecular dynamics simulations, we determined the Y269 residue acts to anchor the intercalating loop on abasic DNA. Atomic force microscopy reveals the Y269 residue is required for proper DNA bending by APE1, providing evidence for the importance of this mechanism. We conclude that this previously unappreciated tyrosine residue is key to anchoring the intercalating loop and stabilizing the DNA in the APE1 active site.
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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.