Affinage

APEX2

DNA-(apurinic or apyrimidinic site) endonuclease 2 · UniProt Q9UBZ4

Length
518 aa
Mass
57.4 kDa
Annotated
2026-06-09
100 papers in source corpus 23 papers cited in narrative 23 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

APE2 (APEX2) is a multifunctional DNA repair nuclease that processes 3'-blocking DNA lesions and links damage processing to checkpoint signaling (PMID:32516598, PMID:23754435). Biochemically it carries strong 3'-5' exonuclease and 3'-phosphodiesterase activities together with only weak AP endonuclease activity, all dependent on the active-site residue Asp277, and it preferentially acts on mismatched or blocked recessed 3'-termini (PMID:16687656); these activities are governed by an ExoIII-like active-site pocket that distinguishes APE2 from the more potent AP endonuclease APE1 (PMID:15319281). APE2 docks onto PCNA through a C-terminal PIP box, which strongly stimulates its 3'-5' exonuclease and 3'-phosphodiesterase activities and recruits it to oxidative damage foci (PMID:11376153, PMID:19443450), while a second PCNA contact and a C-terminal Zf-GRF zinc-finger domain — a crescent-shaped ssDNA-binding claw appended to the catalytic core — drives 3'-5' single-strand-break end resection to generate RPA-coated ssDNA (PMID:28028224, PMID:29361157). This resected ssDNA recruits the ATR-ATRIP-Rad9-TopBP1-Claspin complex, and APE2 directly binds Chk1 through a motif requiring Ser86, acting as a Claspin-like mediator of ATR-Chk1 checkpoint activation following oxidative stress, replication stress, and double-strand breaks (PMID:23754435, PMID:29361157, PMID:34796173). The same end-processing biochemistry underlies a defined role in reversing 3'-blocking lesions that arise from TOP1 processing of genomic ribonucleotides, rendering APE2 synthetically lethal with BRCA1/BRCA2 loss (PMID:32516598, PMID:30686591), and APE2 additionally functions as an effector of microhomology-mediated end joining via intrinsic flap-cleaving activity epistatic with Pol Theta (PMID:37044098). In adaptive immunity, APE2 converts AID/UNG-generated abasic sites into single-strand breaks to promote somatic hypermutation and immunoglobulin diversification, with its PCNA-binding C-terminus required for this activity (PMID:24927551, PMID:37074207, PMID:18025127). APE2 is itself regulated by MKRN3-mediated K48-linked polyubiquitination at K371 and by Hsp70-Hsp90 chaperone-dependent protein stabilization (PMID:38705397, PMID:35883419), and a mitochondrial pool that binds MYH9 contributes to cisplatin-induced kidney and cochlear toxicity (PMID:33288657, PMID:40464565).

Mechanistic history

Synthesis pass · year-by-year structured walk · 22 steps
  1. 2001 High

    Established where APE2 acts and how it is anchored, showing it is a dual nucleus/mitochondrion protein that physically engages PCNA in repair foci.

    Evidence Subcellular fractionation, EM immunocytochemistry, reciprocal Co-IP and in vitro pull-down with PCNA in HeLa cells

    PMID:11376153

    Open questions at the time
    • Functional consequence of PCNA binding not yet defined
    • Mitochondrial role not characterized
  2. 2002 High

    Defined why APE2 is a weak AP endonuclease relative to APE1, attributing substrate specificity across the family to an active-site hydrophobic pocket.

    Evidence Homology modeling and active-site mutagenesis with in vitro endonuclease/exonuclease assays

    PMID:11866537

    Open questions at the time
    • Did not establish APE2's preferred cellular substrate
    • No structure of APE2 itself
  3. 2006 High

    Reframed APE2 as primarily a 3'-5' exonuclease/3'-phosphodiesterase acting on recessed mismatched termini, identifying Asp277 as the catalytic residue for all activities.

    Evidence Reconstituted in vitro biochemical assays with D277A catalytic mutant and multiple substrates

    PMID:16687656

    Open questions at the time
    • In vivo mismatch-processing role not demonstrated
    • Regulation of activity not addressed
  4. 2004 High

    Connected APE2 to organismal proliferation, showing it is required for lymphocyte cell-cycle progression and PCNA-associated late-S-phase function.

    Evidence APEX2-null mouse with flow-cytometric cell-cycle analysis and Co-IP

    PMID:15319281

    Open questions at the time
    • Molecular cause of G2/M accumulation not resolved
    • Link between repair activity and proliferation defect unclear
  5. 2007 High

    Placed APE2 in immunoglobulin class switch recombination as an enzyme converting UNG-generated abasic sites to single-strand breaks during DSB formation.

    Evidence Genetic epistasis with APE1-haploinsufficient mice, CSR flow cytometry, LM-PCR DSB detection

    PMID:18025127

    Open questions at the time
    • Relative APE1/APE2 contribution debated in later work
    • Which catalytic activity is used in vivo not isolated
  6. 2009 High

    Showed PCNA selectively stimulates APE2's 3'-5' exonuclease/phosphodiesterase activities (not AP endonuclease) and that APE2 redistributes to foci on oxidative stress, tying its enzymology to oxidative damage repair.

    Evidence In vitro assays +/- PCNA, fluorescence microscopy of H2O2-treated cells, 8-oxoG substrate processing

    PMID:19443450

    Open questions at the time
    • Downstream pathway from foci recruitment not defined
    • Specificity of stimulation mechanism not structurally resolved
  7. 2009 Medium

    Clarified the CSR mechanism, showing APE-generated SSBs require MMR to become DSBs and that Pol beta competes to repair them in G1.

    Evidence Genetic epistasis in primary B cells with LM-PCR and cell-cycle/mutation assays

    PMID:19010771

    Open questions at the time
    • Overlaps with prior CSR study
    • APE2-specific versus APE1 contribution not separated
  8. 2009 Medium

    Identified APE2 as the dominant APE driving somatic hypermutation via its 3'-5' exonuclease activity, while challenging a strict requirement for either APE in CSR.

    Evidence Apex2-deficient mouse with sequencing-based SHM, plus Apex1 knockdown in CH12F3-2 cells

    PMID:19556307

    Open questions at the time
    • Contradicts earlier CSR findings
    • System-dependence of CSR result unresolved
  9. 2013 High

    Established APE2 as a direct mediator of ATR-Chk1 checkpoint signaling, defining the PIP-box-dependent recruitment, resection-driven RPA-ssDNA generation, and a Claspin-like Chk1-binding role requiring Ser86.

    Evidence Xenopus egg extract immunodepletion, Chk1 phosphorylation and RPA-ssDNA assays, Co-IP, PIP-box and S86A mutants

    PMID:23754435

    Open questions at the time
    • Human cell validation pending at this stage
    • Structural basis of Chk1 binding undefined
  10. 2014 High

    Refined the SHM mechanism, showing germinal-center-enriched APE2 produces SSB entry points for MSH2-MSH6-recruited exonuclease and translesion polymerases generating A:T mutations.

    Evidence Multiple mouse KO combinations (APE2, UNG/APE2 double) with sequencing-based SHM analysis and immunofluorescence

    PMID:24927551

    Open questions at the time
    • Direct biochemical handoff to MMR not reconstituted
    • Role of mismatch versus abasic substrate not separated
  11. 2016 High

    Provided the structural basis for ssDNA recognition, showing the Zf-GRF domain is a crescent-shaped ssDNA-binding claw that regulates 3'-5' resection and is required for RPA recruitment and ATR-Chk1 activation.

    Evidence X-ray crystallography, NMR, SAXS, Zf-GRF mutagenesis, in vitro exonuclease assays, Xenopus checkpoint assays

    PMID:28028224

    Open questions at the time
    • Structure of full-length APE2 not solved
    • Coordination between catalytic core and Zf-GRF not visualized
  12. 2018 High

    Extended checkpoint signaling to a defined single-strand break and revealed a second Zf-GRF-PCNA interaction that organizes resection and checkpoint complex assembly.

    Evidence Xenopus HSS site-specific SSB system, immunodepletion, Co-IP, Zf-GRF/PCNA pull-downs, Chk1 phosphorylation

    PMID:29361157

    Open questions at the time
    • Stoichiometry of dual PCNA contacts unresolved
    • Human cellular validation limited
  13. 2019 High

    Identified APE2 as a synthetic-lethal dependency of BRCA2-deficient cells, requiring its endonuclease activity and PCNA-binding domain, defining a distinct repair pathway needed when HR fails.

    Evidence shRNA/CRISPR genetic screens in BRCA2-isogenic cells with domain-mutant rescue and viability assays

    PMID:30686591

    Open questions at the time
    • Nature of the lethal lesion not yet identified
    • Mechanism distinguishing APE2 from APE1 unclear at this stage
  14. 2020 High

    Defined the lesion driving BRCA synthetic lethality, showing APE2's core role is reversing 3'-blocking lesions from TOP1 processing of genomic ribonucleotides.

    Evidence Genome-wide genetic interaction profiling, biochemistry on 3'-blocked substrates, structural analysis, epistasis with TDP1/TOP1/RNaseH2

    PMID:32516598

    Open questions at the time
    • Full-length human APE2-DNA structure not resolved
    • Other sources of 3'-blocking lesions not enumerated
  15. 2022 High

    Visualized the catalytic mechanism using the yeast ortholog Apn2, showing a DNA-fraying wedge-and-cut mechanism for processing Top1-generated ribonucleotide lesions.

    Evidence X-ray Apn2-DNA complex structures, DNA-wedge mutants, biochemical assays, yeast genetics in RER-defective backgrounds

    PMID:36198268

    Open questions at the time
    • Direct human APE2-DNA complex not solved
    • Conservation of wedge mechanism in human enzyme assumed from orthology
  16. 2022 Medium

    Identified post-translational control of APE2 abundance through the Hsp70-Hsp90 chaperone axis, conserved from yeast to human.

    Evidence Co-IP (Apn2-Ssa1/Hsp82, APE2-Hsp70/Hsp90), chaperone inhibitor treatment with protein-stability Westerns

    PMID:35883419

    Open questions at the time
    • Co-chaperone specificity in human cells not fully mapped
    • Effect of chaperone loss on repair function not measured
  17. 2023 High

    Established APE2 as an effector of microhomology-mediated end joining via intrinsic flap-cleaving activity epistatic with Pol Theta.

    Evidence MMEJ reporter and telomere deprotection assays, APE2-PolQ epistasis, in vitro flap cleavage, nuclease-dead and domain-deletion mutants

    PMID:37044098

    Open questions at the time
    • The domain required for DSB recruitment is uncharacterized
    • Order of APE2 versus PolQ action not resolved
  18. 2023 Medium

    Dissected domain requirements in SHM, showing the PCNA-binding C-terminus promotes SHM and CSR while the Zf-GRF (checkpoint) domain is dispensable, and that APE1 downregulation permissively enables SHM.

    Evidence Primary murine B cells with apex1+/- and APE2-overexpression genetics, domain mutants, sequencing-based SHM

    PMID:37074207

    Open questions at the time
    • Engineered expression context may not reflect native germinal center
    • Mechanistic basis of APE1 suppression unclear
  19. 2024 High

    Defined how APE2 levels are negatively regulated, identifying MKRN3 as the E3 ligase mediating K48-linked polyubiquitination at K371 targeting APE2 for proteasomal degradation.

    Evidence K48-linkage ubiquitination assays, K371R mutant, in vitro reconstitution with MKRN3, Co-IP, stability Westerns

    PMID:38705397

    Open questions at the time
    • Physiological signal triggering MKRN3-APE2 turnover unknown
    • Impact on repair/checkpoint outcomes not measured
  20. 2020 Medium

    Revealed a non-canonical mitochondrial pathology role, showing cisplatin-upregulated APE2 binds MYH9 to drive mitochondrial fragmentation and acute kidney injury.

    Evidence APE2 transgenic and KO mice, cisplatin treatment, pulldown-MS identifying MYH9, Co-IP, histopathology

    PMID:33288657

    Open questions at the time
    • Link between APE2-MYH9 binding and mitochondrial fragmentation not reconstituted in vitro
    • Relationship to APE2's nuclease function unclear
  21. 2025 Medium

    Extended the APE2-MYH9 toxicity axis to cochlear hair cells, mapping MYH9-binding domains and linking APE2 to cisplatin-induced hearing loss and an ATR-p53 apoptotic response.

    Evidence Inducible hair-cell APE2 transgenic mice, EM, Co-IP with domain mapping, APE2 knockdown, mitochondrial/apoptosis/p53 assays

    PMID:40464565

    Open questions at the time
    • Mechanistic link between MYH9 binding and mitochondrial/apoptotic effects not reconstituted
    • Single lab, in vivo overexpression model
  22. 2025 Medium

    Expanded the substrate repertoire, showing human APE2 (with TREX2) can cleave 3'-DNA-peptide cross-links derived from abasic sites.

    Evidence In vitro cleavage assays with chemically synthesized 3'-histone-DPC substrates and purified APE2/TREX2

    PMID:41257340

    Open questions at the time
    • No mutagenesis or in vivo validation
    • Cellular relevance of 3'-DPC repair by APE2 not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • The identity of the domain mediating APE2 recruitment to double-strand breaks, and how its multiple roles (checkpoint, MMEJ, ribonucleotide lesion repair, immunoglobulin diversification) are coordinated and toggled in vivo, remain unresolved.
  • DSB-recruitment domain uncharacterized [#18]
  • No full-length human APE2-DNA structure
  • Integration/regulation of competing functions not defined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140097 catalytic activity, acting on DNA 5 GO:0016787 hydrolase activity 3 GO:0060090 molecular adaptor activity 2 GO:0003677 DNA binding 1
Localization
GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2 GO:0005739 mitochondrion 2
Pathway
R-HSA-1643685 Disease 4 R-HSA-73894 DNA Repair 4 R-HSA-168256 Immune System 3 R-HSA-8953897 Cellular responses to stimuli 3
Partners
CHEK1HSP90AA1HSPA1AMKRN3MYH9PCNATREX2

Evidence

Reading pass · 23 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 Human APE2 protein localizes predominantly to the nucleus and partially to mitochondria; its N-terminal 15 amino acids function as a mitochondrial targeting sequence (MTS). APE2 contains a functional PCNA-binding motif in its C-terminal region, demonstrated by immunoprecipitation and in vitro pull-down assays, and co-localizes with PCNA in nuclear foci. Treatment with HAT medium containing deoxyuridine increased APE2-PCNA co-localization, suggesting a role in PCNA-dependent base excision repair. Subcellular fractionation, Western blot, electron microscopic immunocytochemistry, immunoprecipitation, in vitro pull-down, laser scanning immunofluorescence microscopy, GFP-fusion construct expression in HeLa cells Nucleic acids research High 11376153
2002 Ape2 (human) shares homology with E. coli ExoIII but exhibits comparatively weak AP site-specific endonuclease and 3'-nuclease activities compared to Ape1. Substitutions in the hydrophobic active-site pocket of Ape1 (F266, W280, L282) dramatically reduce abasic incision potency, and introduction of an ExoIII-like pocket into Ape2 enhances its AP endonuclease function. Mutations at F266 and W280 of Ape1 increase 3'-5' exonuclease activity, indicating this pocket governs substrate specificity across the enzyme family. Homology modeling, site-directed mutagenesis, in vitro endonuclease and exonuclease activity assays Journal of molecular biology High 11866537
2004 APEX2-null mice display growth retardation (~80% body size), dyshematopoiesis, and severe lymphopoiesis defects. Both thymocytes and mitogen-stimulated splenocytes from APEX2-null mice accumulate in G2/M phase, demonstrating that APEX2 is required for proper cell cycle progression of proliferating lymphocytes. APEX2 associates with PCNA and its expression peaks in late S phase. Gene knockout in mice (homologous recombination in ES cells), flow cytometry (cell cycle analysis), immunoprecipitation, Western blot, mRNA expression analysis Blood High 15319281
2006 Human Ape2 possesses strong 3'-5' exonuclease and 3'-phosphodiesterase activities and only weak AP endonuclease activity. Mutation of the active-site residue Asp277 to Ala inactivates all these activities. Ape2 preferentially acts on mismatched deoxyribonucleotides at the recessed 3'-termini of partial DNA duplexes, suggesting a role as a 3'-5' exonuclease involved in mismatch processing. In vitro biochemical assays (3'-5' exonuclease, 3'-phosphodiesterase, AP endonuclease), active-site mutagenesis (D277A) Nucleic acids research High 16687656
2007 Both APE1 and APE2 function in immunoglobulin class switch recombination (CSR) to generate the double-strand breaks (DSBs) necessary for CSR in vivo. APE2-deficient mice haploinsufficient for APE1 show reduced CSR and DSBs in switch-region DNA, demonstrating that abasic sites generated by UNG are converted to single-strand breaks by APEs as a step in DSB formation during CSR. Genetic epistasis using APE2-knockout and APE1-haploinsufficient mice, CSR assay (flow cytometry for Ig isotype switching), DSB measurement (ligation-mediated PCR) The Journal of experimental medicine High 18025127
2009 PCNA strongly stimulates the 3'-5' exonuclease and 3'-phosphodiesterase activities of Ape2 but has no effect on its AP endonuclease activity. Upon hydrogen-peroxide treatment, Ape2 redistributes to nuclear foci and co-localizes with PCNA. Biochemically, Ape2 can remove 3'-adenine opposite 8-oxoG, suggesting PCNA-dependent participation in oxidative DNA damage repair. In vitro enzymatic assays with and without PCNA, fluorescence microscopy of H2O2-treated cells, co-localization analysis Nucleic acids research High 19443450
2009 APE1 and APE2 convert abasic sites generated by UNG into single-strand breaks (SSBs) in immunoglobulin switch-region DNA during CSR. Mismatch repair is additionally required to convert distal SSBs into DSBs. DNA polymerase beta attempts to correctly repair APE-generated SSBs in switching B cells, but the high frequency of AID-instigated breaks results in net DSB and mutation generation. S region DSBs are introduced and resolved during G1 phase. Genetic epistasis (APE1/APE2-deficient B cells), ligation-mediated PCR for DSB detection, cell-cycle analysis, mutation frequency assays Philosophical transactions of the Royal Society of London. Series B, Biological sciences Medium 19010771
2009 Apex2 deficiency in mice causes a drastic reduction in somatic hypermutation (SHM) frequency and mutations per clone without affecting the pattern of base substitution, suggesting Apex2 promotes SHM through its 3'-5' exonuclease activity. Unexpectedly, CSR efficiency was not reduced in Apex2-deficient B cells, and Apex1 knockdown in CH12F3-2 cells also did not reduce CSR, indicating neither APE alone is required for CSR in this system. Apex2-deficient mouse model, SHM frequency quantification by sequencing, CSR assay, Apex1 shRNA knockdown in B lymphoma cells International immunology Medium 19556307
2013 APE2 is required for ATR-Chk1 checkpoint activation in response to oxidative stress (H2O2) in Xenopus egg extracts. APE2 is necessary for generation of RPA-bound single-stranded DNA, recruitment of the ATR-ATRIP-Rad9 checkpoint complex to damage sites, and Chk1 phosphorylation. The PCNA-interaction protein (PIP) box of APE2 is essential for its recruitment to H2O2-damaged chromatin. APE2's 3'-phosphodiesterase and 3'-5' exonuclease activities drive 3'-5' SSB end resection to generate ssDNA. APE2 directly associates with Chk1, and Ser86 in its Chk1-binding motif is essential for Chk1 phosphorylation, indicating a Claspin-like mediator role. Xenopus egg extract system, immunodepletion of APE2, Chk1 phosphorylation assay, RPA-ssDNA formation assay, checkpoint protein recruitment assay, co-immunoprecipitation (APE2-Chk1), domain/motif mutagenesis (PIP box mutant, S86A mutant) Proceedings of the National Academy of Sciences of the United States of America High 23754435
2014 APE2 (but not APE1) is highly expressed in germinal center B cells and contributes to somatic hypermutation (SHM) frequency, A:T mutations, insertions, and deletions. In the absence of both UNG and APE2, A:T mutations are dramatically reduced. APE2-generated SSBs serve as entry points for exonuclease recruited by MSH2-MSH6 mismatch repair proteins, which can recruit translesion polymerases to create mutations. APE1 is expressed at low levels in germinal center B cells and has little effect on SHM. APE2-deficient mice, APE1-haploinsufficient mice, SHM frequency and pattern analysis by sequencing, UNG/APE2 double-deficient mice, immunofluorescence for protein expression Proceedings of the National Academy of Sciences of the United States of America High 24927551
2016 APE2's C-terminal Zf-GRF domain is a nucleic acid (particularly ssDNA)-binding module that regulates APE2's 3'-5' resection activity after oxidative DNA damage. X-ray crystallography of the Zf-GRF domain revealed a crescent-shaped ssDNA-binding claw flexibly appended to the EEP catalytic core. Structure-guided Zf-GRF mutations impair APE2 DNA binding and 3'-5' exonuclease processing, and prevent efficient APE2-dependent RPA recruitment to damaged chromatin and ATR-Chk1 DDR activation in Xenopus egg extracts. X-ray crystallography (Zf-GRF domain structure), NMR (nucleic acid binding), SAXS, site-directed mutagenesis of Zf-GRF, in vitro exonuclease activity assays, Xenopus egg extract checkpoint activation assays, RPA chromatin recruitment assay Proceedings of the National Academy of Sciences of the United States of America High 28028224
2018 APE2 promotes ATR-Chk1 DDR signaling from a site-specific single-strand break (SSB). APE2 interacts with PCNA via its PIP box, and a novel mode of APE2-PCNA interaction was identified via the APE2 Zf-GRF domain and PCNA C-terminus. The Zf-GRF-PCNA interaction facilitates 3'-5' SSB end resection, checkpoint protein complex assembly (ATR, ATRIP, TopBP1, Rad9, Claspin), and SSB-induced ATR-Chk1 signaling. SSB-induced ATR DDR is also essential for SSB repair. Xenopus HSS (high-speed supernatant) system with plasmid-based site-specific SSB, immunodepletion, co-immunoprecipitation, in vitro pull-down assays (Zf-GRF/PCNA), checkpoint activation assay (Chk1 phosphorylation) Nucleic acids research High 29361157
2019 BRCA2-deficient cells are synthetically lethal with APEX2 (APE2) loss. BRCA2-deficient cells specifically require the apurinic endonuclease activity and the PCNA-binding domain of APE2 (but not APE1) for viability, placing APE2 in a distinct repair pathway essential when HR is compromised. shRNA and CRISPR-based genetic screen in BRCA2-isogenic cell lines, domain function analysis (endonuclease-dead mutants, PCNA-binding mutant), cell viability assays Molecular cell High 30686591
2020 The primary role of APE2 is to reverse blocked 3'-DNA ends (3'-blocking lesions) that preclude DNA synthesis. APE2 deficiency is synthetically lethal with BRCA1/BRCA2 loss because BRCA-deficient cells are exquisitely sensitive to 3'-blocking lesions. TOP1 processing of genomic ribonucleotides is identified as the main source of 3'-blocking lesions relevant to the APEX2-BRCA1/2 synthetic lethality. Structural and biochemical dissection defines APE2's activity on blocked 3' termini. Genetic interaction profiling (genome-wide screens), biochemical assays on 3'-blocked DNA substrates, structural analysis of APE2, genetic epistasis with TDP1, TOP1, and RNaseH2 Molecular cell High 32516598
2020 Cisplatin treatment upregulates APE2 in proximal tubule cells; APE2 binds to myosin heavy-chain 9 (MYH9) in mitochondria, leading to MYH9 dysfunction and mitochondrial fragmentation contributing to cisplatin-induced acute kidney injury (AKI). APE2-knockout mice are protected from cisplatin-induced AKI. APE2 transgenic mice recapitulate AKI pathophysiology in the absence of cisplatin. APE2 transgenic and knockout mouse models, cisplatin treatment, APE2 pulldown-mass spectrometry (identification of MYH9 as binding partner), co-immunoprecipitation (APE2-MYH9), histopathology, kidney function assays Cancer research Medium 33288657
2021 APE2 is a general regulator of the ATR-Chk1 DDR pathway in human pancreatic cancer cells in response to oxidative stress, DNA replication stress, and DNA double-strand breaks. APE2 knockdown enhances γH2AX foci and micronuclei formation. Celastrol was identified as an APE2 inhibitor that specifically blocks APE2 (but not APE1) binding to ssDNA and inhibits APE2 3'-5' exonuclease activity. Celastrol impairs ATR-Chk1 DDR in both Xenopus egg extracts and human pancreatic cancer cells. APE2 siRNA knockdown in pancreatic cancer cells, γH2AX foci and micronuclei assay (fluorescence microscopy), Xenopus egg extract DDR assay, in vitro ssDNA-binding and exonuclease activity assays with Celastrol, cell viability assays Frontiers in cell and developmental biology Medium 34796173
2022 X-ray crystal structures of yeast Apn2 (ortholog of human APE2) in complex with DNA reveal that Apn2 frays and cleaves 3'-DNA termini via a wedging mechanism that facilitates 1-6 nucleotide endonucleolytic cleavages. APN2 deletion or DNA-wedge mutant strains display mutator phenotypes, cell growth defects, and genotoxic stress sensitivity in a ribonucleotide excision repair (RER)-defective background, demonstrating that Apn2 processes Top1-generated complex DNA lesions at ribonucleotides via a wedge-and-cut mechanism. X-ray crystallography (Apn2-DNA complex structures), biochemical endonuclease/exonuclease assays, site-directed mutagenesis (DNA-wedge mutants), yeast genetic assays (mutation rate, growth, genotoxin sensitivity in RER-defective backgrounds) Cell reports High 36198268
2022 APE2 (and its yeast ortholog Apn2) are clients of the Hsp70-Hsp90 chaperone axis. Apn2 physically interacts with Ssa1 (Hsp70) and Hsp82 (Hsp90) and the co-chaperone Ydj1 in yeast. Human APE2 also binds to Hsp70 and Hsp90 in mammalian cells. Pharmacological inhibition of Hsp70/Hsp90 leads to rapid loss of APE2 protein in cancer cell lines, demonstrating chaperone-dependent APE2 stability. Co-immunoprecipitation (Apn2-Ssa1, Apn2-Hsp82, APE2-Hsp70/Hsp90), small molecule chaperone inhibitor treatment, Western blot for protein stability across cancer cell lines Biomolecules Medium 35883419
2023 APE2 is an effector of microhomology-mediated end joining (MMEJ). Loss of APE2 inhibits MMEJ at deprotected telomeres and at intra-chromosomal DSBs and is epistatic with Pol Theta (PolQ) for MMEJ activity. APE2 possesses intrinsic flap-cleaving nuclease activity, and its MMEJ function in cells depends on nuclease activity. An uncharacterized domain is required for APE2 recruitment to DSBs. MMEJ reporter assay, telomere deprotection assay, APE2 loss-of-function (knockout/knockdown), epistasis with Pol Theta, in vitro flap-cleavage assays, domain-deletion and nuclease-dead mutants, DSB recruitment assay Molecular cell High 37044098
2023 In primary murine B cell cultures, APE2 promotes AID-dependent somatic hypermutation (SHM), while APE1 suppresses SHM. When GC-level APE1/APE2 expression is engineered (reduced APE1 genetically + overexpressed APE2), AID-dependent VDJH4 intron SHM becomes detectable. The C-terminus of APE2 that interacts with PCNA promotes both SHM and CSR, but the Zf-GRF domain (required for ATR-Chk1 interaction) is not required for SHM. APE1 downregulation in GC is required permissively for SHM. Primary murine B cell cultures, genetic manipulation (apex1+/- mice, APE2 overexpression), SHM frequency and pattern analysis by sequencing, domain/motif mutants (PCNA-binding mutant, Zf-GRF mutant) Journal of immunology Medium 37074207
2024 APE2 protein abundance is regulated by ubiquitin-mediated proteasomal degradation. APE2 is poly-ubiquitinated via K48-linked chains, with K371 identified as the key ubiquitination site. MKRN3 was identified and validated as the E3 ubiquitin ligase responsible for APE2 ubiquitination both in cells and in vitro. Ubiquitination assay (K48-linkage-specific antibodies, proteasome inhibitor treatment), site-directed mutagenesis (K371R mutant), in vitro ubiquitination reconstitution assay with MKRN3, co-immunoprecipitation, Western blot for protein stability The Journal of biological chemistry High 38705397
2025 APE2 directly interacts with MYH9 in cochlear outer hair cells following cisplatin treatment. APE2 overexpression alone (using an inducible transgenic mouse model) is sufficient to cause high-frequency hearing loss with hair cell loss and stereocilia disorganization. Critical MYH9-binding domains of APE2 were mapped. APE2 depletion preserved mitochondrial metabolism and protected cochlear cells from cisplatin-induced apoptosis, and activated an ATR-p53 signaling axis promoting nuclear p53 localization. Inducible outer hair cell-specific APE2 transgenic mouse model, electron microscopy (stereocilia ultrastructure), co-immunoprecipitation (APE2-MYH9), domain mapping, APE2 knockdown in cochlear cells, mitochondrial metabolism assay, apoptosis assay, p53 localization by immunofluorescence Cancer research communications Medium 40464565
2025 Human APE2 (along with TREX2) can repair 3'-DNA-peptide cross-links (3'-histone-DPCs) derived from abasic (AP) sites. APE2 cleaves chemically synthesized adducts resembling proteolyzed Schiff base 3'-histone-DPCs, extending the known substrate repertoire of APE2 to include these complex 3'-blocking lesions. In vitro cleavage assays using chemically synthesized 3'-DPC substrates with purified human APE2 and TREX2 Chemical research in toxicology Medium 41257340

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 Directed evolution of APEX2 for electron microscopy and proximity labeling. Nature methods 1101 25419960
2016 Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nature protocols 443 26866790
2019 Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets. Molecular cell 170 30686591
2017 Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Nature protocols 153 28796234
2019 Directed Evolution of Split APEX2 Peroxidase. ACS chemical biology 134 30848125
2001 Human APE2 protein is mostly localized in the nuclei and to some extent in the mitochondria, while nuclear APE2 is partly associated with proliferating cell nuclear antigen. Nucleic acids research 131 11376153
2007 APE1- and APE2-dependent DNA breaks in immunoglobulin class switch recombination. The Journal of experimental medicine 129 18025127
2002 Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III. Journal of molecular biology 110 11866537
2006 Human Ape2 protein has a 3'-5' exonuclease activity that acts preferentially on mismatched base pairs. Nucleic acids research 106 16687656
2013 APE2 is required for ATR-Chk1 checkpoint activation in response to oxidative stress. Proceedings of the National Academy of Sciences of the United States of America 93 23754435
2020 Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and Are Reversed by the APE2 Nuclease. Molecular cell 90 32516598
2019 Expanding APEX2 Substrates for Proximity-Dependent Labeling of Nucleic Acids and Proteins in Living Cells. Angewandte Chemie (International ed. in English) 84 31240809
2021 Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum. Nature communications 69 34381044
2021 APEX2-based Proximity Labeling of Atox1 Identifies CRIP2 as a Nuclear Copper-binding Protein that Regulates Autophagy Activation. Angewandte Chemie (International ed. in English) 66 34550632
2009 Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5' exonuclease activities of human Ape2 in repair of oxidative DNA damage. Nucleic acids research 66 19443450
2018 Single-Strand Break End Resection in Genome Integrity: Mechanism and Regulation by APE2. International journal of molecular sciences 59 30110897
2016 APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress. Proceedings of the National Academy of Sciences of the United States of America 54 28028224
2016 Proximity-dependent biotin labelling in yeast using the engineered ascorbate peroxidase APEX2. The Biochemical journal 51 27274088
2018 APE2 promotes DNA damage response pathway from a single-strand break. Nucleic acids research 47 29361157
2019 Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system. Nucleic acids research 46 30805613
2014 Differential expression of APE1 and APE2 in germinal centers promotes error-prone repair and A:T mutations during somatic hypermutation. Proceedings of the National Academy of Sciences of the United States of America 46 24927551
2017 APEX2-enhanced electron microscopy distinguishes sigma-1 receptor localization in the nucleoplasmic reticulum. Oncotarget 44 28881650
2009 The roles of APE1, APE2, DNA polymerase beta and mismatch repair in creating S region DNA breaks during antibody class switch. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 42 19010771
2004 Growth retardation and dyslymphopoiesis accompanied by G2/M arrest in APEX2-null mice. Blood 40 15319281
2019 Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane. The Journal of biological chemistry 38 31519755
2020 Cisplatin-Mediated Upregulation of APE2 Binding to MYH9 Provokes Mitochondrial Fragmentation and Acute Kidney Injury. Cancer research 35 33288657
2017 Optimizing the fragment complementation of APEX2 for detection of specific protein-protein interactions in live cells. Scientific reports 35 28955036
2023 The APE2 nuclease is essential for DNA double-strand break repair by microhomology-mediated end joining. Molecular cell 34 37044098
2009 Apex2 is required for efficient somatic hypermutation but not for class switch recombination of immunoglobulin genes. International immunology 34 19556307
2020 An Optimized Protocol for Proximity Biotinylation in Confluent Epithelial Cell Cultures Using the Peroxidase APEX2. STAR protocols 32 33111110
2020 Wnt-inducible Lrp6-APEX2 interacting proteins identify ESCRT machinery and Trk-fused gene as components of the Wnt signaling pathway. Scientific reports 30 33299006
2021 An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. The Journal of cell biology 27 33306092
2020 Genomic alterations and abnormal expression of APE2 in multiple cancers. Scientific reports 25 32111912
2003 Characterization of the genomic structure and expression of the mouse Apex2 gene. Genomics 25 12573260
2023 Once-Daily Oral Berotralstat for Long-Term Prophylaxis of Hereditary Angioedema: The Open-Label Extension of the APeX-2 Randomized Trial. The journal of allergy and clinical immunology. In practice 21 38122865
2021 APEX2 Proximity Proteomics Resolves Flagellum Subdomains and Identifies Flagellum Tip-Specific Proteins in Trypanosoma brucei. mSphere 21 33568455
2019 APEX2-mediated proximity labeling resolves protein networks in Saccharomyces cerevisiae cells. The FEBS journal 21 31323700
2018 Proximity Labeling by a Recombinant APEX2-FGF1 Fusion Protein Reveals Interaction of FGF1 with the Proteoglycans CD44 and CSPG4. Biochemistry 20 29812912
2020 Function and molecular mechanisms of APE2 in genome and epigenome integrity. Mutation research. Reviews in mutation research 19 34083046
2021 Defining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. Genomics, proteomics & bioinformatics 18 34555496
2021 APE2 Is a General Regulator of the ATR-Chk1 DNA Damage Response Pathway to Maintain Genome Integrity in Pancreatic Cancer Cells. Frontiers in cell and developmental biology 16 34796173
2023 Proteomics from compartment-specific APEX2 labeling in Mycobacterium tuberculosis reveals Type VII secretion substrates in the cell wall. Cell chemical biology 14 37967559
2019 Periplasmic Nanobody-APEX2 Fusions Enable Facile Visualization of Ebola, Marburg, and Mĕnglà virus Nucleoproteins, Alluding to Similar Antigenic Landscapes among Marburgvirus and Dianlovirus. Viruses 14 31010013
2019 The cysteine-free single mutant C32S of APEX2 is a highly expressed and active fusion tag for proximity labeling applications. Protein science : a publication of the Protein Society 14 31306516
2015 An enhanced ascorbate peroxidase 2/antibody-binding domain fusion protein (APEX2-ABD) as a recombinant target-specific signal amplifier. Chemical communications (Cambridge, England) 14 26063640
2020 Identification of APEX2 as an oncogene in liver cancer. World journal of clinical cases 12 32775374
2021 Identification of cellular proteins interacting with PEDV M protein through APEX2 labeling. Journal of proteomics 11 33757879
2021 Apurinic/Apyrimidinic Endonuclease 2 (APE2): An ancillary enzyme for contextual base excision repair mechanisms to preserve genome stability. Biochimie 11 34302888
2017 Determining the target protein localization in 3D using the combination of FIB-SEM and APEX2. Biophysics reports 11 29238746
1997 Ortho-vanadate affects both the tyrosination/detyrosination state of spindle microtubules and the organization of XTH-2 spindles. European journal of cell biology 11 9270873
1988 Scanning microfluorometric measurement of cell constituents. Principles of the method and its application to the determination of NAD content and redox state of XTH-2 cells in culture. Histochemistry 11 3366666
2021 Optimized APEX2 peroxidase-mediated proximity labeling in fast- and slow-growing mycobacteria. Methods in enzymology 10 35331378
2020 Probing the Environment of Emerin by Enhanced Ascorbate Peroxidase 2 (APEX2)-Mediated Proximity Labeling. Cells 10 32138363
2019 Identification of Lipid Droplet Proteomes by Proximity Labeling Proteomics Using APEX2. Methods in molecular biology (Clifton, N.J.) 10 31124088
2024 Using the heme peroxidase APEX2 to probe intracellular H2O2 flux and diffusion. Nature communications 9 38336829
2023 APE2: catalytic function and synthetic lethality draw attention as a cancer therapy target. NAR cancer 8 36755963
2020 The GABARAP Co-Secretome Identified by APEX2-GABARAP Proximity Labelling of Extracellular Vesicles. Cells 8 32560054
2025 A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins. Nucleic acids research 7 39718986
2024 APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Scientific reports 7 38755230
2022 Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Cell reports 6 36198268
2020 Three-Dimensional Visualization of APEX2-Tagged Erg11 in Saccharomyces cerevisiae Using Focused Ion Beam Scanning Electron Microscopy. mSphere 6 32024705
2020 Selective Visualization of Caveolae by TEM Using APEX2. Methods in molecular biology (Clifton, N.J.) 6 32548814
2018 Nano-structural analysis of engrafted human induced pluripotent stem cell-derived cardiomyocytes in mouse hearts using a genetic-probe APEX2. Biochemical and biophysical research communications 6 30333092
2022 Visualizing Filoviral Nucleoproteins Using Nanobodies Fused to the Ascorbate Peroxidase Derivatives APEX2 and dEAPX. Methods in molecular biology (Clifton, N.J.) 5 35157287
2022 APEX2-Mediated Proximity Labeling Resolves the DDIT4-Interacting Proteome. International journal of molecular sciences 5 35563580
2024 Detecting Native Protein-Protein Interactions by APEX2 Proximity Labeling in Drosophila Tissues. Bio-protocol 4 39512889
2023 Clickable APEX2 Probes for Enhanced RNA Proximity Labeling in Live Cells. Analytical chemistry 4 38099807
2022 In vivo Proximity Labeling of Nuclear and Nucleolar Proteins by a Stably Expressed, DNA Damage-Responsive NONO-APEX2 Fusion Protein. Frontiers in molecular biosciences 4 35733943
2022 The APE2 Exonuclease Is a Client of the Hsp70-Hsp90 Axis in Yeast and Mammalian Cells. Biomolecules 4 35883419
2018 Adapting dCas9-APEX2 for subnuclear proteomic profiling. Methods in enzymology 4 30691651
2024 Ligand-Dependent Mechanisms of CC Chemokine Receptor 5 (CCR5) Trafficking Revealed by APEX2 Proximity Labeling Proteomics. bioRxiv : the preprint server for biology 3 37961097
2024 Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Computational and structural biotechnology journal 3 38298178
2024 An APEX2-based proximity-dependent biotinylation assay with temporal specificity to study protein interactions during autophagy in the yeast Saccharomyces cerevisiae. Autophagy 3 38958087
2024 Protocol to profile spatially resolved NLRP3 inflammasome complexes using APEX2-based proximity labeling. STAR protocols 3 39460941
2023 APE2 Promotes AID-Dependent Somatic Hypermutation in Primary B Cell Cultures That Is Suppressed by APE1. Journal of immunology (Baltimore, Md. : 1950) 3 37074207
2023 Identification of Substrates of Secreted Bacterial Protease by APEX2-Based Proximity Labeling. Methods in molecular biology (Clifton, N.J.) 3 37258967
2023 APEX2-Mediated Proximity Labeling of Wnt Receptor Interactors Upon Pathway Activation. microPublication biology 3 37260921
2025 Cisplatin-Induced APE2 Overexpression Disrupts MYH9 Function and Causes Hearing Loss. Cancer research communications 2 40464565
2025 APEX2 proximity labeling of RNA in bacteria. Cell reports methods 2 41118767
2024 Identification of Protein Partners by APEX2 Proximity Labeling. Methods in molecular biology (Clifton, N.J.) 2 37930538
2024 Ubiquitin-mediated regulation of APE2 protein abundance. The Journal of biological chemistry 2 38705397
2023 Localization of Mitochondrial Nucleoids by Transmission Electron Microscopy Using the Transgenic Expression of the Mitochondrial Helicase Twinkle and APEX2. Methods in molecular biology (Clifton, N.J.) 2 36807792
2023 Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Molecular biology of the cell 2 37792491
2022 Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semipermeabilized Cells. Methods in molecular biology (Clifton, N.J.) 2 35524122
2025 Antibody-Mediated Protein A-APEX2 Labeling (AMAPEX) for Proximity Proteome Exploration. Methods in molecular biology (Clifton, N.J.) 1 40638056
2025 APEX2-based quantitative proteomics of LAT and CD3ζ interactomes in living human Jurkat T cells unveils new interactors. Journal of cell science 1 40694042
2025 Contrasting roles of APE1 and APE2 in genome maintenance, cancer development, and therapeutic targeting. NAR cancer 1 41446759
2024 Protocols for identifying endogenous interactors of RNA-binding proteins in mammalian cells using the peroxidase APEX2 biotin-labeling method. STAR protocols 1 39392747
2010 Molecular diagnosis of Down syndrome using quantitative APEX-2 microarrays. Prenatal diagnosis 1 20949644
1999 Protein kinase C affects reformation of endothelial junctions in xenopus XTH-2 cells. Cell biology international 1 10527549
2026 Identification of the Subcompartment-Specific Mitochondrial Proteome by APEX2 Proximity Labeling in Saccharomyces cerevisiae. Bio-protocol 0 41769260
2026 Directed Evolution Improves the Catalytic Efficiency of APEX2-Mediated Proximity-Dependent RNA Labeling. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 0 41903118
2025 APEX2 proximity labeling of RNA in bacteria. bioRxiv : the preprint server for biology 0 39345536
2025 Identification of MCM2-Interacting Proteins Associated with Replication Initiation Using APEX2-Based Proximity Labeling Technology. International journal of molecular sciences 0 39940790
2025 APEX2 RNA Proximity Labeling in Mammalian Cell Lines With Low Biotin Permeability. Bio-protocol 0 40655423
2025 Comprehensive analysis of the role of ASC1 and APE2 introns on cellular fitness, transcription, and post-transcriptional dynamics. The FEBS journal 0 41131709
2025 Human APE2 and TREX2 Repair 3'-DNA-Peptide Cross-links Derived from Abasic Sites. Chemical research in toxicology 0 41257340
2025 APEX2 and TurboID define unique subcellular proteomes. Scientific reports 0 41372295
2024 APEX2-Mediated Proximity Protein Labeling in Dictyostelium. Methods in molecular biology (Clifton, N.J.) 0 38954202
2018 Publisher Correction: Optimizing the fragment complementation of APEX2 for detection of specific protein-protein interactions in live cells. Scientific reports 0 29892021

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