Affinage

PNKP

Bifunctional polynucleotide phosphatase/kinase · UniProt Q96T60

Length
521 aa
Mass
57.1 kDa
Annotated
2026-06-10
68 papers in source corpus 25 papers cited in narrative 25 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

PNKP is a bifunctional DNA repair enzyme that processes damaged DNA termini through its DNA 5'-kinase and 3'-phosphatase activities, generating ligatable ends required across single-strand break repair (SSBR), non-homologous end joining (NHEJ), and DNA replication (PMID:10446192, PMID:32504494). It is recruited to single-strand breaks through a bipartite mechanism in which its FHA domain (notably Arg35/Arg48) binds CK2-phosphorylated XRCC1 with high affinity to tether the proteins, while a second low-affinity contact through the XRCC1 RIR motif stimulates PNKP kinase activity; PARP1/PARP2-dependent ADP-ribosylation underpins this recruitment to oxidative breaks (PMID:28453785, PMID:28821613, PMID:27965414, PMID:29100039, PMID:33220551). In NHEJ, the same FHA domain and a phosphatase-domain surface engage CK2-phosphorylated XRCC4-LigIV, positioning PNKP within multifunctional end-processing synaptic complexes (PMID:28453785, PMID:33220551). PNKP abundance and localization are tightly regulated: ATM-mediated phosphorylation at S114/S126 blocks Cul4A-DDB1-STRAP-dependent proteasomal degradation, importin-alpha mediates its nuclear import, and PFKFB3-derived fructose-2,6-bisphosphate acts as a required cofactor for its catalytic activity (PMID:23042680, PMID:37061005, PMID:39298485). PNKP also functions at replication forks, where CDK1/2 phosphorylation (including at T118) directs it to ssDNA gaps for Okazaki fragment maturation and PARP1-dependent backup gap filling, and where it protects stalled forks from TOP1-dependent nascent DNA degradation (PMID:39395804, PMID:40146629, PMID:39671289). Loss of PNKP function causes human disease: distinct mutations underlie MCSZ, AOA4, and CMT2B2, with reduced phosphatase activity correlating with neurodevelopmental dysfunction and reduced kinase activity with neurodegeneration (PMID:22508754, PMID:32504494, PMID:37061005). PNKP integrity is also compromised in polyglutamine disorders, where mutant ATXN3 and HTT impair PNKP within transcription-coupled repair complexes, driving DNA break accumulation and aberrant ATM signaling (PMID:25590633, PMID:30994454).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 1999 High

    Established the core biochemical identity of PNKP as a single enzyme carrying two distinct DNA-end-processing activities, defining its fundamental role in restoring repair-competent termini.

    Evidence GST-PNKP in vitro kinase/phosphatase assays plus E. coli xth nfo complementation

    PMID:10446192

    Open questions at the time
    • Did not define recruitment partners or pathway context in mammalian cells
    • No structural basis for substrate selection
  2. 2012 High

    Linked PNKP enzymatic and stability defects to human disease, showing that disease mutations reduce kinase/phosphatase activity, lower protein levels, and impair cellular strand break repair.

    Evidence Recombinant mutant enzyme assays, Western blotting, and strand break repair assays in MCSZ patient cells

    PMID:22508754

    Open questions at the time
    • Mechanism linking specific activity loss to neuronal phenotype not resolved here
    • Did not distinguish SSBR vs DSBR contributions
  3. 2012 High

    Defined how PNKP abundance is controlled by a damage-responsive switch, showing ATM phosphorylation stabilizes PNKP against Cul4A-DDB1-STRAP-mediated degradation.

    Evidence Phospho-site mapping, ubiquitylation assays, Cul4A-DDB1-STRAP purification, Strap-/- MEFs

    PMID:23042680

    Open questions at the time
    • Stoichiometry and kinetics of the stabilization switch not quantified
    • Whether other kinases contribute is unaddressed
  4. 2015 High

    Connected PNKP dysfunction to polyglutamine neurodegeneration, showing mutant ATXN3 binds and inactivates PNKP upstream of ATM-p53-PKCδ apoptotic signaling.

    Evidence Co-IP, PNKP activity assays, ATM-inhibitor and PNKP-overexpression rescue in SCA3 cell and mouse models

    PMID:25590633

    Open questions at the time
    • Molecular basis of mutant ATXN3-mediated inactivation undefined
    • Generalizability to other polyQ proteins not yet shown
  5. 2017 High

    Resolved how PNKP is integrated into both NHEJ and SSBR through FHA-domain interactions with phosphorylated XRCC4-LigIV and XRCC1, and established a bipartite tethering/stimulation model.

    Evidence SAXS, HDX-MS, recombinant complex assays, RIR mutagenesis, and laser-microirradiation recruitment in human cells

    PMID:27965414 PMID:28453785 PMID:28821613 PMID:29100039

    Open questions at the time
    • High-resolution structure of full complexes not obtained
    • Quantitative contribution of each interaction in vivo not fully partitioned
  6. 2018 Medium

    Extended the XRCC1-PNKP interaction beyond the canonical phospho-segment and tied common XRCC1 SNPs to reduced PNKP recruitment and stimulation.

    Evidence Biochemical binding/activity assays with XRCC1 fragments and SNP variants plus laser-microirradiation recruitment

    PMID:30446622

    Open questions at the time
    • Structural basis of the extended interaction not determined
    • Physiological impact of SNPs at organismal level unaddressed
  7. 2019 High

    Placed PNKP within an HTT-organized transcription-coupled repair complex, showing mutant HTT impairs PNKP and causes break accumulation in transcribed genes.

    Evidence Co-IP of HTT/POLR2A/ATXN3/PNKP/CBP complex, activity assays, and PNKP rescue in HD cell and mouse models

    PMID:30994454

    Open questions at the time
    • Precise architecture of the TCR complex unresolved
    • How transcription couples to PNKP loading not mechanistically defined
  8. 2020 High

    Mapped genotype-to-pathway relationships across PNKP-linked diseases and proved an essential role for the FHA domain in recruitment and genome stability.

    Evidence Comet/γH2AX repair assays in patient fibroblasts with domain-specific complementation, plus FHA point mutants and XRCC1/XRCC4 depletion with cytogenetic readouts

    PMID:32504494 PMID:33220551

    Open questions at the time
    • Why phosphatase loss preferentially drives neurodevelopmental vs kinase loss neurodegenerative phenotypes not mechanistically explained
  9. 2023 High

    Revealed that subcellular localization, not catalysis, is the defect in AOA4, establishing importin-alpha-dependent nuclear import as essential for PNKP function.

    Evidence In vitro activity assays, immunofluorescence, importin alpha/beta Co-IP, and patient PBMC Western blots

    PMID:37061005

    Open questions at the time
    • Nuclear localization signal not precisely mapped
    • Whether import is regulated dynamically during the cell cycle unknown
  10. 2024 High

    Identified a metabolic cofactor requirement for PNKP, showing PFKFB3-derived fructose-2,6-bisphosphate is needed for activity and is deficient in polyQ disease brains.

    Evidence PFKFB3 Co-IP, F2,6BP supplementation and depletion in nuclear/mitochondrial extracts, Kd measurement, and Drosophila HD rescue

    PMID:39298485 PMID:bio_10.1101_2024.11.04.621834

    Open questions at the time
    • Allosteric mechanism by which F2,6BP modulates catalysis not structurally defined
    • Whether cofactor levels are dynamically regulated under stress unclear
  11. 2024 High

    Defined a replication-associated role for PNKP at forks, including Okazaki fragment maturation, PCNA association, and protection of stalled forks from TOP1-dependent degradation.

    Evidence iPOND, PCNA Co-IP, CDK1/2 kinase and phospho-site assays, DNA fiber analysis, and TOP1/TDP1 epistasis

    PMID:39395804 PMID:39671289 PMID:40146629

    Open questions at the time
    • Relative importance of replicative vs repair functions in tissues not weighed
    • Coordination between fork-protection and gap-filling roles undefined
  12. 2023 Medium

    Proposed acetylation as a pathway-partitioning code, with p300-mediated K142 directing BER/SSBR and CBP-mediated K226 directing DSBR.

    Evidence Site-specific acetylation mapping, acetyl-specific Co-IP and ChIP, p300/CBP knockdown, and non-acetylable mutant cells (preprint)

    PMID:37645927

    Open questions at the time
    • Preprint status; awaits peer-reviewed confirmation
    • How acetylation switches partner selection mechanistically unresolved
  13. 2025 Medium

    Extended PNKP's repair role to NHEJ synaptic architecture and to mitochondrial and transcription-coupled NHEJ complexes, while uncovering non-canonical roles in ZIKV replication, atherosclerosis, and TNBC ferroptosis.

    Evidence Cryo-EM of NHEJ synaptic complex with Pol λ and PNKP (preprint), Co-IP of TC-NHEJ and mitochondrial repair complexes (preprints), and Co-IP/functional assays for DDOST, STAT3, and ZIKV NS1 interactions

    PMID:35412344 PMID:40501590 PMID:40743845 PMID:41109654 PMID:bio_10.1101_2024.09.19.613927 PMID:bio_10.1101_2025.07.24.666629

    Open questions at the time
    • Several findings are preprints or single-lab studies
    • Non-canonical PNKP functions outside DNA repair are not mechanistically integrated with its enzymatic activity

Open questions

Synthesis pass · forward-looking unresolved questions
  • How PNKP's multiple regulatory layers — phosphorylation, acetylation, nuclear import, and metabolic cofactor supply — are integrated to partition the single enzyme among SSBR, NHEJ, replication, and mitochondrial repair in different cell types remains unresolved.
  • No unified structural model of regulated pathway selection
  • Tissue-specific determinants of PNKP function in neurons vs proliferating cells unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140097 catalytic activity, acting on DNA 3 GO:0003677 DNA binding 2 GO:0016740 transferase activity 2 GO:0016787 hydrolase activity 2
Localization
GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2 GO:0005739 mitochondrion 2
Pathway
R-HSA-1643685 Disease 5 R-HSA-73894 DNA Repair 4 R-HSA-69306 DNA Replication 3
Partners
ATXN3HTTLIG4PCNAPFKFB3POLR2AXRCC1XRCC4
Complex memberships
HTT mitochondrial DNA repair complexHTT/POLR2A/ATXN3/PNKP/CBP transcription-coupled repair complexNHEJ short-range synaptic complexXRCC4-LigIV NHEJ complex

Evidence

Reading pass · 25 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 PNKP encodes a bifunctional enzyme with both DNA 5'-kinase and DNA 3'-phosphatase activities. A GST-PNKP fusion protein displayed both activities in vitro, and the 3'-phosphatase domain shows similarity to L-2-haloacid dehalogenases. PNKP expression rescued oxidative-damage sensitivity in E. coli xth nfo double mutants, demonstrating in vivo removal of 3'-phosphate groups to generate termini suitable for DNA polymerase. GST-fusion protein in vitro kinase/phosphatase assays, E. coli complementation rescue experiment, tryptic peptide sequencing from bovine enzyme The Journal of biological chemistry High 10446192
2012 MCSZ-associated PNKP mutations (L176F, T424Gfs48X, exon15Δfs4X, E326K) reduce or ablate DNA kinase activity in vitro and reduce cellular PNKP protein levels ~10-fold; all mutations result in reduced rates of chromosomal DNA strand break repair in cells. L176F also reduces phosphatase activity, while E326K destabilizes PNKP at physiological temperature. Recombinant PNKP in vitro kinase and phosphatase assays, Western blotting for cellular protein levels, chromosomal DNA strand break repair assays in patient-derived cells Nucleic acids research High 22508754
2012 ATM phosphorylates PNKP at serines 114 and 126 in response to oxidative DNA damage, inhibiting ubiquitylation-dependent proteasomal degradation of PNKP and increasing its stability. The Cul4A-DDB1 ubiquitin ligase complex (with STRAP as adaptor) is responsible for PNKP ubiquitylation. Strap-/- MEFs have elevated PNKP levels and enhanced resistance to oxidative DNA damage. Phosphorylation site mapping, ubiquitylation assays, purification of Cul4A-DDB1-STRAP complex, Strap-/- mouse embryonic fibroblast analysis Nucleic acids research High 23042680
2017 PNKP forms a stable complex with XRCC4-LigIV in NHEJ. The PNKP FHA domain binds CK2-phosphorylated XRCC4 C-terminal tail; only one PNKP protomer binds per XRCC4 dimer. SAXS reveals a flexible multi-state complex with multipoint contacts between the PNKP FHA and catalytic domains and the XRCC4 coiled-coil/LigIV BRCT repeats. Hydrogen-deuterium exchange identifies a phosphatase domain surface contacting XRCC4-LigIV. The MCSZ-causing E326K mutation on this surface impairs PNKP recruitment to damaged DNA in human cells. Recombinant complex purification, small-angle X-ray scattering (SAXS), hydrogen-deuterium exchange mass spectrometry, laser microirradiation recruitment assay in human cells Nucleic acids research High 28453785
2017 PNKP interacts with XRCC1 via two distinct sites: a high-affinity phosphorylation-dependent interaction through the PNKP FHA domain and a low-affinity interaction through the Rev1-interacting region (RIR) motif in XRCC1 (requiring three conserved phenylalanine residues). The low-affinity interaction stimulates PNKP kinase activity and promotes SSBR and cell survival. A bipartite model is proposed in which the high-affinity interaction tethers XRCC1 and PNKP to enable the stimulatory low-affinity interaction. Biochemical and biophysical interaction assays, mutagenesis of RIR phenylalanines, PNKP kinase activity assays, cell survival and SSBR assays The Journal of biological chemistry High 28821613
2017 PARP1 and PARP2 have overlapping roles in recruiting PNKP and XRCC1 to oxidative single-strand breaks in chromatin. Loss of both PARP1 and PARP2 (but not either alone) greatly reduces or ablates PNKP chromatin binding following H2O2 treatment, demonstrating that very low levels of ADP-ribosylation synthesized by either enzyme are sufficient for PNKP recruitment. Isogenic PARP1/PARP2 double-knockout human diploid cells, chromatin fractionation assays after H2O2 treatment, PARP inhibitor dose-response Nucleic acids research High 27965414
2015 Mutant ATXN3 (expanded polyQ) interacts with and inactivates PNKP in SCA3, resulting in inefficient DNA repair, persistent accumulation of DNA strand breaks, and chronic activation of ATM signaling. Either PNKP overexpression or pharmacological ATM inhibition blocked mutant ATXN3-mediated cell death, placing PNKP upstream of ATM-p53-PKCδ pro-apoptotic signaling. Co-immunoprecipitation of endogenous PNKP with mutant ATXN3, PNKP activity assays, DNA damage accumulation measurement, ATM inhibitor rescue, PNKP overexpression rescue in SCA3 cell and mouse models PLoS genetics High 25590633
2019 HTT forms a transcription-coupled DNA repair (TCR) complex with POLR2A, ATXN3, PNKP, and CBP. Mutant HTT impairs PNKP activity and causes persistent DNA break accumulation in actively transcribed genes, and aberrant ATM activation. Increasing PNKP activity in mutant HTT cells improves genome integrity and cell survival. Co-immunoprecipitation of the TCR complex, PNKP activity assays in HD cell and transgenic mouse models, gene-specific DNA damage quantification, PNKP overexpression rescue eLife High 30994454
2018 PNKP FHA domain interactions with phosphorylated XRCC1 extend beyond the well-characterized residues 515–526. An XRCC1 fragment (residues 166–436) binds PNKP and DNA and efficiently activates PNKP kinase activity. XRCC1 SNP variants R194W and R280H show weaker binding to PNKP and severely reduced stimulation of PNKP activity, and cells expressing these variants show reduced PNKP recruitment to laser-microirradiation-induced damage. Biochemical binding assays, PNKP kinase activity assays with XRCC1 fragments and SNP variants, laser microirradiation live-cell recruitment assay The Journal of biological chemistry Medium 30446622
2017 CK2-mediated phosphorylation of XRCC1 is required for PNKP recruitment to DNA damage sites. A phosphorylation-mutant XRCC1 failed to support PNKP-GFP recruitment to micro-irradiation-induced damage, while cells expressing XRCC1 phosphorylation mutant showed marked reversal of camptothecin hypersensitivity compared to Xrcc1-/- cells, suggesting a backup pathway for PNKP-independent end cleaning. Live-cell fluorescence microscopy of PNKP-GFP at micro-irradiation damage, stable expression of phosphorylation-mutant XRCC1 in Xrcc1-/- fibroblasts, clonogenic survival assay DNA repair Medium 29100039
2020 Pathological PNKP mutations associated with MCSZ, AOA4, and CMT2B2 cause a significant defect in DNA single-strand break repair (SSBR) but not in DNA double-strand break repair (DSBR) in primary patient fibroblasts. Restoration of SSBR requires both PNKP's kinase and phosphatase activities and its FHA domain interaction with XRCC1. Reduced DNA phosphatase activity correlates with neurodevelopmental dysfunction, while reduced DNA kinase activity correlates with neurodegeneration. Alkaline comet assay and γH2AX immunofluorescence for SSBR and DSBR rates in primary patient fibroblasts, complementation with kinase-dead, phosphatase-dead, and FHA-mutant PNKP constructs Nucleic acids research High 32504494
2020 The PNKP FHA domain (specifically Arg35 and Arg48) is essential for PNKP recruitment to DNA damage sites via interactions with XRCC1 and XRCC4. PNKP R35A/R48A mutant failed to accumulate at laser-induced damage tracks, and siRNA depletion of XRCC1 and/or XRCC4 reduced PNKP accumulation. Cells expressing the FHA mutant showed increased sensitivity to ionizing radiation, delayed SSB and DSB repair, and genome instability (micronuclei, chromosome bridges). Laser micro-irradiation with live-cell confocal imaging, siRNA knockdown of XRCC1/XRCC4, PNKP FHA domain point mutants, clonogenic survival, comet assay, γH2AX foci, micronuclei/chromosome bridge scoring Mutation research High 33220551
2023 A conserved glutamine mutation in PNKP causing AOA4 does not significantly reduce enzymatic activities in vitro, but severely abrogates nuclear localization of PNKP. The mutant PNKP fails to interact with importin alpha (but not importin beta), blocking nuclear import. Western blot of AOA4 patient PBMCs confirmed cytoplasmic retention of mutant PNKP. Cells expressing mutant PNKP accumulate DNA double-strand breaks and activate DNA damage response pathways despite normal enzymatic activity. In vitro enzymatic activity assays, immunofluorescence for subcellular localization, co-immunoprecipitation with importin alpha/beta, Western blotting of patient-derived PBMCs, γH2AX assay The Journal of biological chemistry High 37061005
2024 PNKP interacts with the nuclear isoform of PFKFB3, and PFKFB3's product fructose-2,6-bisphosphate (F2,6BP) acts as a cofactor that is required for PNKP activity. PFKFB3 depletion markedly abrogates PNKP activity without changing its protein level. F2,6BP levels are significantly lower in nuclear extracts from postmortem HD and SCA3 patient brains; supplementation of F2,6BP restored PNKP activity in these extracts and rescued genome integrity and HD phenotypes in Drosophila. Co-immunoprecipitation of PNKP with PFKFB3, PNKP activity assays with/without F2,6BP supplementation in nuclear extracts, PFKFB3 siRNA depletion, rescue in Drosophila HD model Proceedings of the National Academy of Sciences of the United States of America High 39298485
2024 PNKP participates in DNA replication by functioning at replication forks, associating with PCNA, and contributing to Okazaki fragment (OF) maturation. CDK1/2 phosphorylate PNKP at multiple residues; mutation of these phosphorylation sites impairs PNKP function in DNA replication. Cellular depletion of PNKP produces defects similar to those of other OFM-related proteins. iPOND/replication fork enrichment, co-immunoprecipitation with PCNA, CDK1/2 kinase assays with PNKP, phosphorylation site mutagenesis, replication fork dynamics assays after PNKP depletion The Journal of biological chemistry Medium 39395804
2025 CDK-mediated phosphorylation of PNKP at threonine 118 (T118) is required for PNKP recruitment to ssDNA gaps between Okazaki fragments during DNA replication. T118A-expressing cells accumulate ssDNA gaps in S phase and show accelerated replication fork progression. PNKP is involved in PARP1-dependent replication gap filling as a backup pathway when OF ligation is impaired. T118A phospho-site mutagenesis, ssDNA gap detection in S phase, replication fork progression assays (DNA fiber analysis), PARP1-dependent gap filling assay eLife High 40146629
2024 PNKP localizes at stalled replication forks and protects them from nucleolytic degradation of nascent DNA. Loss of PNKP leads to TOP1-dependent nascent DNA degradation at stalled forks (distinct from the BRCA2-dependent pathway). Hydroxyurea treatment causes ribonucleotide misincorporation that traps TOP1 at stalled forks; reducing TOP1 or TDP1 reverses nascent DNA degradation in PNKP-deficient cells. iPOND for fork localization, DNA fiber analysis for nascent strand degradation, epistasis with BRCA2, TDP1 and TOP1 knockdown rescue experiments Cell reports High 39671289
2025 Cryo-EM structure of the NHEJ short-range synaptic complex shows Pol λ and PNKP simultaneously bound to the complex, demonstrating that NHEJ can form large multifunctional end-processing complexes. The structure reveals the mode of Pol λ recruitment and establishes coordinated end-processing by both factors at the short-range synaptic complex. Cryo-EM structure determination of NHEJ short-range synaptic complex with Pol λ and PNKP bioRxivpreprint Medium 40501590
2022 ZIKV infection relocalizes PNKP from the nucleus to the cytoplasm in neural progenitor cells (NPC), colocalizing with ZIKV replication factory marker NS1, causing functional nuclear PNKP depletion and DNA damage accumulation. Two PNKP phosphatase inhibitors or PNKP knockout inhibited ZIKV replication, indicating PNKP is a host factor required for ZIKV replication. Immunofluorescence colocalization of PNKP with NS1 in infected NPC, PNKP inhibitors and PNKP knockout to assess ZIKV replication, γH2AX for DNA damage, Chk1/Chk2 activation assays Journal of virology Medium 35412344
2025 In atherosclerosis, macrophage-derived exosomal miR-146a-5p suppresses PNKP expression; reduced PNKP decreases its interaction with DDOST, leading to enhanced DDOST phosphorylation and activation of JAGN1-dependent NET formation in neutrophils. Co-immunoprecipitation of PNKP with DDOST, Western blot, qRT-PCR, dual-luciferase reporter, RIP assay in ApoE-/- mouse model and ox-LDL-stimulated macrophages Cellular signalling Medium 41109654
2023 PNKP is acetylated at two lysine residues in different domains: K142 is constitutively acetylated by p300, while K226 is acetylated by CBP only after DSB induction. AcK142-PNKP associates exclusively with BER/SSBR proteins and AcK226-PNKP exclusively with DSBR proteins. Cells expressing non-acetylable K142R or K226R PNKP accumulate DNA damage specifically in transcribed genes. In HD striatal neuronal cells, K142 but not K226 was acetylated, consistent with CBP degradation in HD. Site-specific acetylation identification, Co-IP with acetylation-specific antibodies, p300/CBP knockdown/identification as acetyltransferases, non-acetylable mutant cell lines, γH2AX assay, chromatin-immunoprecipitation with Ac-PNKP antibodies bioRxivpreprint Medium 37645927
2025 HTT organizes a mitochondrial DNA repair complex containing HTT, mitochondrial RNA polymerase, transcription factors, and PNKP. Mutant HTT impairs this complex causing persistent mitochondrial DNA lesions. Restoring PNKP expression in a Drosophila HD model improves mitochondrial genome integrity and ameliorates motor deficits. Co-immunoprecipitation of mitochondrial repair complex components, mitochondrial DNA damage assays, PNKP overexpression rescue in Drosophila HD model bioRxivpreprint Medium bio_10.1101_2025.07.24.666629
2024 PNKP is present in mitochondria and its activity is decreased in mitochondrial extracts from HD patient brains due to reduced PFKFB3 and F2,6BP levels. PFKFB3 is part of a mitochondrial DNA repair complex containing HTT, PNKP, DNA Pol γ (POLG), and Lig IIIα. PNKP binds F2,6BP with Kd ~525 nM. Addition of F2,6BP restored PNKP activity in HD mitochondrial extracts and restored mitochondrial genome integrity in HD cells and Drosophila. Subcellular fractionation and PNKP activity assay in mitochondrial extracts, Co-IP of mitochondrial repair complex, F2,6BP binding assay (Kd measurement), F2,6BP supplementation rescue in HD cells and Drosophila bioRxivpreprint Medium bio_10.1101_2024.11.04.621834
2024 HTT coordinates a Transcription-Coupled NHEJ (TC-NHEJ) complex containing PNKP, Ku70/80, XRCC4, and chromatin remodeler BRG1 to resolve transcription-associated DSBs in brain. HTT recruitment to DSBs in transcriptionally active gene-rich regions is BRG1-dependent, while efficient recruitment of TC-NHEJ proteins including PNKP is HTT-dependent. PNKP overexpression in a Drosophila HD model restores TC-NHEJ, improving genome integrity, motor defects, and lifespan. Co-immunoprecipitation of TC-NHEJ complex, ChIP at DSBs, BRG1/HTT dependency assays by knockdown, PNKP overexpression in Drosophila HD model rescue bioRxivpreprint Medium bio_10.1101_2024.09.19.613927
2025 PNKP targeting in TNBC activates ferroptosis through the autophagic machinery. PNKP and STAT3 are rapidly phosphorylated, colocalize, and interact upon ferroptosis induction or doxorubicin treatment. PNKP inhibition activates STING and inhibits STAT3, increasing ferritinophagy and intracellular iron levels while decreasing GPX4 and SCD1. PNKP inhibition synergized with doxorubicin in TNBC animal models and patient-derived organoids. Co-immunoprecipitation of PNKP with STAT3, immunofluorescence colocalization, transcriptomic profiling, ferroptosis markers (ROS, glutathione, SCD1, GPX4), animal model and organoid therapeutic experiments Redox biology Medium 40743845

Source papers

Stage 0 corpus · 68 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1999 Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage. The Journal of biological chemistry 246 10446192
2010 Mutations in PNKP cause microcephaly, seizures and defects in DNA repair. Nature genetics 233 20118933
2017 Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Nucleic acids research 166 27965414
2015 Mutations in PNKP cause recessive ataxia with oculomotor apraxia type 4. American journal of human genetics 109 25728773
2019 Mutant huntingtin impairs PNKP and ATXN3, disrupting DNA repair and transcription. eLife 107 30994454
2015 Inactivation of PNKP by mutant ATXN3 triggers apoptosis by activating the DNA damage-response pathway in SCA3. PLoS genetics 72 25590633
2012 Progressive cerebellar atrophy and polyneuropathy: expanding the spectrum of PNKP mutations. Neurogenetics 68 23224214
2012 Impact of PNKP mutations associated with microcephaly, seizures and developmental delay on enzyme activity and DNA strand break repair. Nucleic acids research 61 22508754
2016 Polynucleotide kinase-phosphatase (PNKP) mutations and neurologic disease. Mechanisms of ageing and development 50 27125728
2017 Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex. Nucleic acids research 47 28453785
2012 Phosphorylation of PNKP by ATM prevents its proteasomal degradation and enhances resistance to oxidative stress. Nucleic acids research 38 23042680
2020 Pathological mutations in PNKP trigger defects in DNA single-strand break repair but not DNA double-strand break repair. Nucleic acids research 34 32504494
2018 The polynucleotide kinase 3'-phosphatase gene (PNKP) is involved in Charcot-Marie-Tooth disease (CMT2B2) previously related to MED25. Neurogenetics 28 30039206
2015 Mutation in PNKP presenting initially as axonal Charcot-Marie-Tooth disease. Neurology. Genetics 26 27066567
2012 The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family. Proceedings of the National Academy of Sciences of the United States of America 25 22308407
2014 Causative novel PNKP mutations and concomitant PCDH15 mutations in a patient with microcephaly with early-onset seizures and developmental delay syndrome and hearing loss. Journal of human genetics 22 24965255
2018 Targeting DNA repair with PNKP inhibition sensitizes radioresistant prostate cancer cells to high LET radiation. PloS one 20 29320576
2019 From congenital microcephaly to adult onset cerebellar ataxia: Distinct and overlapping phenotypes in patients with PNKP gene mutations. American journal of medical genetics. Part A 18 31436889
2012 Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair. Proceedings of the National Academy of Sciences of the United States of America 18 22847431
2022 Zika Virus Induces Mitotic Catastrophe in Human Neural Progenitors by Triggering Unscheduled Mitotic Entry in the Presence of DNA Damage While Functionally Depleting Nuclear PNKP. Journal of virology 17 35412344
2018 Nanoencapsulation of Novel Inhibitors of PNKP for Selective Sensitization to Ionizing Radiation and Irinotecan and Induction of Synthetic Lethality. Molecular pharmaceutics 17 29688721
2018 Domain analysis of PNKP-XRCC1 interactions: Influence of genetic variants of XRCC1. The Journal of biological chemistry 17 30446622
2012 Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system. RNA (New York, N.Y.) 17 23118415
2019 Novel PNKP mutations causing defective DNA strand break repair and PARP1 hyperactivity in MCSZ. Neurology. Genetics 16 31041400
2017 Novel PNKP mutation in siblings with ataxia-oculomotor apraxia type 4. Journal of neurogenetics 16 28552035
2017 The Rev1 interacting region (RIR) motif in the scaffold protein XRCC1 mediates a low-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNA single-strand break repair. The Journal of biological chemistry 16 28821613
2022 Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor. Scientific reports 15 35354845
2019 Ataxia with Oculomotor Apraxia Type 4 with PNKP Common "Portuguese" and Novel Mutations in Two Belarusian Families. Journal of pediatric genetics 15 31061747
2017 XRCC1-mediated repair of strand breaks independent of PNKP binding. DNA repair 14 29100039
2013 Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system. Nucleic acids research 14 23595150
2021 A synthetically lethal nanomedicine delivering novel inhibitors of polynucleotide kinase 3'-phosphatase (PNKP) for targeted therapy of PTEN-deficient colorectal cancer. Journal of controlled release : official journal of the Controlled Release Society 13 33933518
2020 The Phenotypic Spectrum of PNKP-Associated Disease and the Absence of Immunodeficiency and Cancer Predisposition in a Dutch Cohort. Pediatric neurology 13 32980744
2018 Rare compound heterozygous variants in PNKP identified by whole exome sequencing in a German patient with ataxia-oculomotor apraxia 4 and pilocytic astrocytoma. Clinical genetics 13 29498415
2018 Multi affected pedigree with congenital microcephaly: WES revealed PNKP gene mutation. Brain & development 13 30195441
2020 The FHA domain of PNKP is essential for its recruitment to DNA damage sites and maintenance of genome stability. Mutation research 12 33220551
2024 Plasma pQTL and brain eQTL integration identifies PNKP as a therapeutic target and reveals mechanistic insights into migraine pathophysiology. The journal of headache and pain 11 39578729
2023 Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans. The Journal of biological chemistry 11 37061005
2013 Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkp•hen1 RNA repair system. Biochemistry 11 23721485
2011 Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs. RNA (New York, N.Y.) 11 22190744
2021 PNKP is required for maintaining the integrity of progenitor cell populations in adult mice. Life science alliance 9 34226276
2021 Nano-Delivery of a Novel Inhibitor of Polynucleotide Kinase/Phosphatase (PNKP) for Targeted Sensitization of Colorectal Cancer to Radiation-Induced DNA Damage. Frontiers in oncology 9 35004293
2021 Discovery of potential inhibitors targeting the kinase domain of polynucleotide kinase/phosphatase (PNKP): Homology modeling, virtual screening based on multiple conformations, and molecular dynamics simulation. Computational biology and chemistry 8 34456161
2019 PNKP deficiency mimicking a benign hereditary chorea: The misleading presentation of a neurodegenerative disorder. Parkinsonism & related disorders 8 30956058
2016 Microcephalic primordial dwarfism in an Emirati patient with PNKP mutation. American journal of medical genetics. Part A 8 27232581
2024 Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and ameliorates neurodegenerative symptoms in Huntington's disease. Proceedings of the National Academy of Sciences of the United States of America 7 39298485
2020 Mutational survivorship bias: The case of PNKP. PloS one 7 33332469
2023 Novel PNKP mutations associated with reduced DNA single-strand break repair and severe microcephaly, seizures, and developmental delay. Molecular genetics & genomic medicine 5 37916443
2021 Prenatal phenotype of PNKP-related primary microcephaly associated with variants affecting both the FHA and phosphatase domain. European journal of human genetics : EJHG 5 34697416
2025 PNKP targeting engages the autophagic machinery through STING and STAT3 to potentiate ferroptosis and chemotherapy in TNBC. Redox biology 4 40743845
2024 CDK-dependent phosphorylation regulates PNKP function in DNA replication. The Journal of biological chemistry 4 39395804
2019 Compound Heterozygous Mutations in PNKP Gene in an Iranian Child with Microcephaly, Seizures, and Developmental Delay. Fetal and pediatric pathology 4 31707899
2024 PNKP safeguards stalled replication forks from nuclease-dependent degradation during replication stress. Cell reports 3 39671289
2013 PNKP knockdown by RNA interference inhibits herpes simplex virus-1 replication in astrocytes. Virologica Sinica 3 24213989
2025 CDK-mediated phosphorylation of PNKP is required for end-processing of single-strand DNA gaps on Okazaki fragments and genome stability. eLife 2 40146629
2025 End Processing in NHEJ by Polymerase λ and PNKP is coordinated during short-range synapsis. bioRxiv : the preprint server for biology 2 40501590
2025 Macrophage-derived exosome miR-146a-5p modulates PNKP/DDOST/JAGN1 complex to regulate NETs formation in atherosclerosis. Cellular signalling 2 41109654
2024 Characterization of Two Novel PNKP Splice-Site Variants in a Proband With Microcephaly, Intellectual Disability, and Multiple Malformations. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2 39417375
2025 Prenatal phenotype of PNKP-related microcephaly, seizures, and developmental delay: A case report and literature review. Medicine 1 39833032
2024 Synergistic Nanomedicine Delivering Topoisomerase I Toxin (SN-38) and Inhibitors of Polynucleotide Kinase 3'-Phosphatase (PNKP) for Enhanced Treatment of Colorectal Cancer. Molecular pharmaceutics 1 38785196
2015 Expression of Cyclin d1 protein and CCND1 та PNKP genes in peripheral blood mononuclear cells in clean up worker of Chornobyl accident with different state of immune system. Problemy radiatsiinoi medytsyny ta radiobiolohii 1 26695908
2026 Refining the phenotypic spectrum of PNKP-related microcephaly: a study of 27 new patients. Journal of medical genetics 0 41436176
2026 Microcephaly, seizures and developmental delay caused by two novel mutations in the PNKP gene: a case report. Translational pediatrics 0 41982948
2026 Deficiency of pnkp in zebrafish causes microcephaly, seizures, and developmental delay through mitochondrial dysfunction. Zoological research 0 41983441
2025 B-cell immunodeficiency associated with polynucleotide kinase 3'-phosphatase (PNKP) deficiency. The journal of allergy and clinical immunology. Global 0 40687947
2025 Compound Heterozygous PNKP Variants Causing Developmental and Epileptic Encephalopathy with Severe Microcephaly: Natural History of Two New Cases and Literature Review. NeuroSci 0 41283299
2024 Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and ameliorates neurodegenerative symptoms in Huntington's disease. bioRxiv : the preprint server for biology 0 37961108
2023 Site-specific acetylation of polynucleotide kinase 3'-phosphatase (PNKP) regulates its distinct role in DNA repair pathways. bioRxiv : the preprint server for biology 0 37645927
2022 Self-Supplying Guide RNA-Mediated CRISPR/Cas12a Fluorescence System for Sensitive Detection of T4 PNKP. Molecules (Basel, Switzerland) 0 36558152

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