Affinage

PAXX

Protein PAXX · UniProt Q9BUH6

Length
204 aa
Mass
21.6 kDa
Annotated
2026-06-10
33 papers in source corpus 17 papers cited in narrative 17 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/7 claims corpus-supported (71%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PAXX (C9orf142) is an accessory factor of the classical non-homologous end-joining (NHEJ) pathway and a structural paralog of XRCC4 that promotes repair of DNA double-strand breaks (DSBs) (PMID:25574025). Its principal molecular role is to engage the DSB-recognition machinery directly: PAXX binds Ku through a C-terminal motif that contacts Ku70 specifically, forming a stable PAXX–Ku–DNA ternary complex that requires a bare DNA extension and that drives accumulation of Ku at breaks in cells (PMID:27705800, PMID:28051062, PMID:37256950). High-resolution cryo-EM and crystallographic analysis define the Ku70/PAXX interface and show that PAXX and XLF can bind the Ku heterodimer simultaneously, acting as alternative structural bridges in DNA-PK end-bridging dimers to promote DNA end synapsis (PMID:37256950, PMID:40546969). Through its N-terminal head domain, PAXX—like its paralogs XRCC4 and XLF—interacts with and stimulates DNA polymerase λ and is required for its recruitment to damage sites, facilitating gap-filling and joining of incompatible ends (PMID:30250067). Functionally, PAXX is largely redundant with XLF and partially with DNA-PKcs: loss of PAXX alone produces only modest DSB-repair defects, but combined PAXX/XLF deficiency abolishes end joining and is synthetic-lethal in mice, causing embryonic lethality, genomic instability, CNS apoptosis, and a near-complete block in lymphocyte development that phenocopies Xrcc4 or Lig4 loss (PMID:27601299, PMID:27601633, PMID:27798842). Genetic interplay extends to XRCC4 itself, as PAXX is redundant with XRCC4–XLF filaments during V(D)J recombination (PMID:34519267). The stability of the PAXX–Ku interface is rate-limiting for NHEJ of complex, end-processing-requiring DSBs, with interface-stabilizing mutations accelerating repair of radiation-induced breaks (PMID:40659092).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2015 High

    Established PAXX as a previously unrecognized NHEJ factor by showing it is a structural paralog of XRCC4 that binds Ku and promotes Ku-dependent end ligation, defining its place in the core repair machinery.

    Evidence Crystal structure, direct binding and in vitro ligation assays, and CRISPR/RNAi KO with DSB-sensitivity and chromatin-assembly readouts

    PMID:25574025 PMID:25941166

    Open questions at the time
    • Did not resolve which Ku subunit PAXX contacts
    • Magnitude of contribution relative to XLF/XRCC4 not established
  2. 2016 High

    Defined the molecular basis of PAXX's Ku engagement, showing a Ku70-specific, DNA-dependent ternary complex and that its ligation-stimulating role is weak and unmasked only when XLF is absent.

    Evidence Biochemical reconstitution of PAXX–Ku–DNA complex, co-IP, in vitro ligation assays in PAXX-deficient cells

    PMID:27705800

    Open questions at the time
    • Atomic-resolution interface not yet defined
    • Quantitative redundancy with XLF not mapped genetically
  3. 2016 High

    Resolved why PAXX single loss is mild by demonstrating functional redundancy with XLF—combined deficiency abolishes DSB joining and V(D)J recombination, while PAXX alone does not phenocopy core factor loss and acts independently of ATM/RAG.

    Evidence CRISPR/genetic KO mouse models and G1-arrested pro-B cell lines, V(D)J and class-switch assays, IR sensitivity, epistasis with ATM/RAG, Ku-binding mutants

    PMID:27601299 PMID:27601633 PMID:27798842

    Open questions at the time
    • Mechanistic distinction between PAXX and XLF activities not yet defined
    • Basis for synthetic lethality at the molecular level unresolved
  4. 2017 High

    Assigned PAXX and XLF distinct, complementary molecular tasks—PAXX promotes Ku accumulation at DSBs whereas XLF enhances LIG4 recruitment—and confirmed the developmental consequences of combined loss in vivo.

    Evidence Mouse KO models with live-cell imaging/ChIP of Ku and LIG4 dynamics, epistasis with ATM/DNA-PK inhibitors

    PMID:28051062

    Open questions at the time
    • How PAXX stabilizes Ku mechanistically not structurally explained
    • Whether the two functions are strictly separable or overlap partially
  5. 2018 High

    Extended PAXX function beyond Ku tethering to gap-filling, showing PAXX (with XRCC4 and XLF) binds and stimulates DNA polymerase λ via its N-terminal head domain and is required for Pol λ recruitment to damage.

    Evidence Co-IP/interactome mapping, in vitro polymerase activity assay, laser micro-irradiation recruitment, incompatible end-joining assay

    PMID:30250067

    Open questions at the time
    • Relative contribution of each paralog to Pol λ stimulation in vivo not quantified
    • Structural basis of the head domain–Pol λ contact not defined
  6. 2018 Medium

    Probed cell-context dependence of PAXX, finding it largely dispensable for CSR and basal NHEJ in some human and mouse systems, and reported lower-confidence links to base excision repair via Pol β and a viral restriction role against HSV-1.

    Evidence Genetic KO with DSB/CSR and chromosomal-break readouts; Co-IP with Pol β and TMZ sensitivity; HSV-1 infection localization and replication assays

    PMID:29144403 PMID:29511621 PMID:30238427

    Open questions at the time
    • Pol β/BER link rests on a single Co-IP without reconstitution or domain mapping
    • HSV-1 restriction mechanism distinct from NHEJ not defined
    • Cell-type basis for variable PAXX dependence unexplained
  7. 2019 Medium

    Refined the epistatic map in human cells, showing PAXX—unlike XLF—does not genetically interact with DNA-PKcs or overlap with ATM, distinguishing its functional niche from other accessory factors.

    Evidence CRISPR single/double KO HAP1 cells, DSB sensitivity, chromosomal break analysis, genetic epistasis; plus Co-IP/small-molecule (M11) chemoresistance study

    PMID:31141305 PMID:31640855

    Open questions at the time
    • Mechanistic reason for lack of DNA-PKcs interaction not explained
    • M11/chemoresistance link is single-lab Co-IP plus inhibitor rescue
  8. 2023 High

    Delivered the atomic-resolution view of the Ku70/PAXX interface and showed PAXX and XLF can co-occupy Ku to form alternate DNA-PK end-bridging dimers, providing a structural model for redundant end-synapsis bridging.

    Evidence Cryo-EM, X-ray crystallography, interface mutagenesis, in vitro and cellular end-joining assays

    PMID:37256950

    Open questions at the time
    • Dynamics of switching between PAXX- and XLF-bridged dimers in cells not resolved
    • Contribution of each bridging mode to repair fidelity not quantified
  9. 2025 Medium

    Connected PAXX–Ku complex stability to repair kinetics, showing an interface-stabilizing substitution accelerates NHEJ of end-processing-requiring DSBs and that PAXX promotes end synapsis partially redundantly with DNA-PKcs and XLF for blunt-end joining.

    Evidence Structure-guided interface mutagenesis with live-cell imaging and repair kinetics; Cas9-reporter end-joining with indel profiling across PAXX/DNA-PKcs/XLF-deficient cells

    PMID:40546969 PMID:40659092

    Open questions at the time
    • Single-lab studies awaiting independent confirmation
    • Physiological significance of nucleolar mislocalization unclear
    • How interface stability tunes repair rate mechanistically not fully defined
  10. 2021 High

    Demonstrated direct functional interplay between PAXX and XRCC4, showing PAXX is redundant with XRCC4–XLF filaments in V(D)J recombination via a filament-deficient XRCC4 separation-of-function allele.

    Evidence Xrcc4-M61R knock-in mouse crossed onto Paxx-/- background, V(D)J and CNS apoptosis assays, genetic epistasis

    PMID:34519267

    Open questions at the time
    • Whether PAXX substitutes structurally for XRCC4-XLF filaments not shown biochemically
    • Molecular basis of the rescue not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the alternate PAXX- and XLF-bridged DNA-PK synaptic complexes are dynamically selected and coordinated during repair of different break types, and whether PAXX's reported BER and viral-restriction roles reflect genuine NHEJ-independent functions, remain open.
  • No real-time structural data on bridging-mode selection in cells
  • BER/Pol β link unconfirmed by reconstitution
  • HSV-1 restriction mechanism undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0003677 DNA binding 2 GO:0098772 molecular function regulator activity 2
Localization
GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2 GO:0005730 nucleolus 1
Pathway
R-HSA-168256 Immune System 4 R-HSA-73894 DNA Repair 4
Partners
DNA-PKCSPOLBPOLLXLFXRCC4XRCC5XRCC6
Complex memberships
DNA-PK end-bridging dimerPAXX-Ku-DNA ternary complex

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2015 PAXX (C9orf142) is a structural paralog of XRCC4, as determined by crystal structure, and directly interacts with Ku to promote DNA double-strand break repair by NHEJ. PAXX promotes Ku-dependent DNA ligation in vitro and facilitates assembly of core NHEJ factors on damaged chromatin in cells. Crystal structure determination, direct binding assay, in vitro ligation assay, RNAi/CRISPR-Cas9 KO with DSB sensitivity phenotype, chromatin fractionation Science High 25574025
2015 XLS/PAXX (c9orf142) co-purifies with DNA-PKcs and other core NHEJ factors (identified by affinity purification-mass spectrometry) and interacts with core NHEJ factors; its depletion impairs DSB repair consistent with an NHEJ defect. Affinity purification–mass spectrometry, co-immunoprecipitation, computational structural modeling, siRNA knockdown with DSB repair assay Cell death and differentiation Medium 25941166
2016 PAXX forms a stable ternary complex with Ku bound to DNA through a direct interaction specifically with Ku70 (not Ku80), and this complex requires a bare DNA extension for stability. PAXX provides only weak stimulation of LIG4/XRCC4 ligation activity, which is unmasked when XLF is absent. Biochemical complex reconstitution, co-immunoprecipitation, in vitro ligation assay, PAXX-deficient cell lines Cell reports High 27705800
2016 PAXX function in V(D)J recombination depends on its interaction with Ku; PAXX and XLF have redundant functions in NHEJ such that combined deficiency abrogates DSB joining, whereas PAXX deficiency alone does not phenocopy loss of core NHEJ factors. Unlike XLF, PAXX's role does not overlap with ATM or the RAG complex. CRISPR/genetic KO mouse models, V(D)J recombination assays, epistasis analysis with ATM/RAG, Ku-binding mutants Cell reports High 27601299
2016 PAXX and XLF are functionally redundant for joining DSBs in G1-arrested pro-B cells during V(D)J recombination; combined PAXX/XLF deficiency abrogates DSB joining and sensitizes cells to ionizing radiation, but PAXX deficiency alone has no impact even in ATM-deficient pro-B lines. CRISPR/genetic KO in G1-arrested mouse pro-B cell lines, V(D)J recombination assay, IR sensitivity assay, class switch recombination assay Proceedings of the National Academy of Sciences of the United States of America High 27601633
2017 PAXX promotes accumulation of KU at DSBs in vivo, while XLF enhances LIG4 recruitment without affecting KU dynamics; these represent distinct but critically complementary molecular functions within NHEJ. Paxx/Xlf double-KO mice show severe genomic instability, neuronal apoptosis, and embryonic lethality. Mouse genetic KO models, live-cell imaging/ChIP for KU and LIG4 dynamics at DSBs, epistasis with ATM/DNA-PK inhibitors Nature communications High 28051062
2016 Paxx loss is epistatic with Ku80, Lig4, and Atm deficiency in mice, but Paxx/Xlf double-knockout is synthetic-lethal in mammals, with embryonic lethality, genomic instability, CNS cell death, and near-complete block in lymphogenesis phenocopying Xrcc4-/- or Lig4-/- mice. Mouse genetic KO models, epistasis analysis across multiple NHEJ-deficient backgrounds Genes & development High 27798842
2018 PAXX, XLF, and XRCC4 share the ability to interact with DNA polymerase λ (Pol λ), stimulate its activity, and are required for recruitment of Pol λ to laser-induced DNA damage sites. This stimulation requires a direct interaction between the SP/8 kDa domain of Pol λ and the N-terminal head domains of XRCC4 paralogs, facilitating recognition of the 5' end of substrate gaps. PAXX and XLF collaborate with Pol λ to promote joining of incompatible DNA ends. Co-immunoprecipitation/interactome mapping, in vitro polymerase activity assay, laser micro-irradiation recruitment assay, incompatible end-joining assay in cells Nature communications High 30250067
2023 Cryo-EM and X-ray crystallography structures of PAXX C-terminal Ku-binding motif bound to Ku70/80 identify residues critical for the Ku70/PAXX interaction in vitro and in cells. PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK end-bridging dimers (mediated by either Ku80 or XLF), providing complementary advantage for DNA end synapsis and end joining. Cryo-EM, X-ray crystallography, mutagenesis of Ku70/PAXX interface residues, in vitro end-joining assay, cellular end-joining assay Science advances High 37256950
2018 PAXX deficiency causes modest sensitivity to DNA damage in human HAP1 cells (unlike XRCC4 or XLF deficiency) and PAXX-deficient murine CH12F3 B cells perform class switch recombination at near-wild-type levels, indicating that PAXX is largely dispensable for CSR and basal NHEJ in these cell systems. Genetic KO (CRISPR, mouse Paxx-/- CH12F3 cells), DSB-inducing agent sensitivity assay, CSR assay, chromosomal break analysis FEBS open bio Medium 29511621
2019 Chemoresistance to doxorubicin or cisplatin in osteosarcoma cells results in enhanced PAXX–Ku70 interaction and elevated NHEJ efficiency; disruption of the PAXX–Ku70 interaction with small molecule M11 re-sensitizes resistant cells to these drugs. Co-immunoprecipitation of PAXX-Ku70 in resistant cells, NHEJ efficiency assay, small-molecule inhibitor (M11) treatment with drug sensitivity assay Biochemical and biophysical research communications Medium 31640855
2018 PAXX interacts with DNA polymerase β (Pol β) and contributes to base excision repair (BER); PAXX-deficient cells show increased sensitivity to the BER-substrate drug temozolomide in glioma cells. Co-immunoprecipitation of PAXX with Pol β, PAXX-deficient cell lines, TMZ sensitivity assay Journal of molecular neuroscience Low 30238427
2017 PAXX is excluded from the nucleus during HSV-1 infection, and PAXX-/- cells show a defect in viral genome replication efficiency but produce greater numbers of infectious virions, indicating PAXX restricts HSV-1 infection in a manner distinct from other c-NHEJ factors. PAXX-/- cell lines, immunofluorescence localization during HSV-1 infection, viral replication and infectious virion production assays Viruses Medium 29144403
2019 In human HAP1 cells, XLF but not PAXX genetically interacts with DNA-PKcs (i.e., XLF/DNA-PKcs double KO is more severe than either single KO, whereas PAXX/DNA-PKcs double KO phenocopies DNA-PKcs single KO). ATM has overlapping functions with DNA-PKcs, XLF, and XRCC4, but not with PAXX, in response to DSBs. CRISPR-generated human HAP1 single and double KO cell lines, DSB-inducing agent sensitivity assay, chromosomal break analysis, genetic epistasis FEBS open bio Medium 31141305
2025 A single conserved amino acid substitution in PAXX at the Ku70/80 contact interface dramatically stabilizes the PAXX–Ku repair complex, causes co-dependent mislocalization of PAXX and Ku to the nucleoli, and accelerates NHEJ repair specifically of DSBs requiring end processing (radiation-induced DSBs), revealing that repair complex stability at the Ku70/PAXX interface is rate-limiting for NHEJ of complex DSBs. Structure-guided mutagenesis of PAXX Ku70/80 interface, live-cell imaging of PAXX and Ku localization, NHEJ repair kinetics assay with radiation-induced vs. restriction enzyme DSBs The Journal of biological chemistry Medium 40659092
2025 PAXX promotes DSB end synapsis during NHEJ in a manner partially redundant with DNA-PKcs and XLF; PAXX becomes important for blunt DSB end joining when DNA-PKcs or XLF is disrupted, but PAXX loss does not magnify the DNA-PKcs-mediated suppression of microhomology-mediated deletions, distinguishing its function from DNA-PKcs in end-use fidelity. Cas9-reporter end-joining assay in PAXX-/-, DNA-PKcs-inhibited, and XLF-/- single and combined-deficient human cell lines; indel profiling iScience Medium 40546969
2021 An XRCC4 separation-of-function mutation (M61R) that abolishes XRCC4–XLF filament formation while preserving LIG4 stabilization reveals that PAXX is functionally redundant with XRCC4-XLF filaments during V(D)J recombination; crossing Xrcc4-M61R mice onto Paxx-/- background causes severe immunodeficiency and embryonic lethality, identifying a direct functional interplay between XRCC4 and PAXX in NHEJ. Xrcc4 separation-of-function knock-in mouse crossed onto Paxx-/- background; V(D)J recombination assay; CNS apoptosis analysis; genetic epistasis eLife High 34519267

Source papers

Stage 0 corpus · 33 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. Science (New York, N.Y.) 248 25574025
2007 Molecular basis of Bcl-xL's target recognition versatility revealed by the structure of Bcl-xL in complex with the BH3 domain of Beclin-1. Journal of molecular biology 159 17659302
2016 PAXX Is an Accessory c-NHEJ Factor that Associates with Ku70 and Has Overlapping Functions with XLF. Cell reports 88 27705800
2017 PAXX promotes KU accumulation at DNA breaks and is essential for end-joining in XLF-deficient mice. Nature communications 86 28051062
2016 PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line. Proceedings of the National Academy of Sciences of the United States of America 86 27601633
2016 Specific Roles of XRCC4 Paralogs PAXX and XLF during V(D)J Recombination. Cell reports 73 27601299
2016 Synthetic lethality between PAXX and XLF in mammalian development. Genes & development 66 27798842
2015 XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair. Cell death and differentiation 58 25941166
2016 Deficiency of XLF and PAXX prevents DNA double-strand break repair by non-homologous end joining in lymphocytes. Cell cycle (Georgetown, Tex.) 40 27830975
2023 PAXX binding to the NHEJ machinery explains functional redundancy with XLF. Science advances 36 37256950
2017 PAXX and Xlf interplay revealed by impaired CNS development and immunodeficiency of double KO mice. Cell death and differentiation 35 29077092
2018 PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair. Nature communications 26 30250067
2019 Genetic interaction between DNA repair factors PAXX, XLF, XRCC4 and DNA-PKcs in human cells. FEBS open bio 25 31141305
2020 miR-548e Sponged by ZFAS1 Regulates Metastasis and Cisplatin Resistance of OC by Targeting CXCR4 and let-7a/BCL-XL/S Signaling Axis. Molecular therapy. Nucleic acids 24 32353736
2018 Normal development of mice lacking PAXX, the paralogue of XRCC4 and XLF. FEBS open bio 22 29511619
2018 Robust DNA repair in PAXX-deficient mammalian cells. FEBS open bio 22 29511621
1997 Immunolocalization of Bcl-xL/S in the central nervous system of neonatal and adult rats. Cell and tissue research 22 9042772
2018 Synthetic lethality between DNA repair factors Xlf and Paxx is rescued by inactivation of Trp53. DNA repair 16 30579708
2019 PAXX is a novel target to overcome resistance to doxorubicin and cisplatin in osteosarcoma. Biochemical and biophysical research communications 15 31640855
2018 PAXX Participates in Base Excision Repair via Interacting with Pol β and Contributes to TMZ Resistance in Glioma Cells. Journal of molecular neuroscience : MN 12 30238427
2021 Supercritical carbon dioxide dried double layer laponite XLS and alginate/polyacrylamide construct and immune response. Tissue & cell 9 34920234
2017 The Non-Homologous End Joining Protein PAXX Acts to Restrict HSV-1 Infection. Viruses 8 29144403
2025 Distinct functions of PAXX and MRI during chromosomal end joining. iScience 6 40546969
2023 Plant PAXX has an XLF-like function and stimulates DNA end joining by the Ku-DNA ligase IV/XRCC4 complex. The Plant journal : for cell and molecular biology 6 37340932
2021 An XRCC4 mutant mouse, a model for human X4 syndrome, reveals interplays with Xlf, PAXX, and ATM in lymphoid development. eLife 6 34519267
2020 An in vivo study of the impact of deficiency in the DNA repair proteins PAXX and XLF on development and maturation of the hemolymphoid system. The Journal of biological chemistry 6 31915249
2020 Non-Homologous End Joining Factors XLF, PAXX and DNA-PKcs Maintain the Neural Stem and Progenitor Cell Population. Biomolecules 6 33379193
2023 C9orf142 transcriptionally activates MTBP to drive progression and resistance to CDK4/6 inhibitor in triple-negative breast cancer. Clinical and translational medicine 5 38009308
2024 Distinct functions of PAXX and MRI during chromosomal end joining. bioRxiv : the preprint server for biology 4 39229097
2020 The Distinct Role of the Extra-Large G Protein ɑ-Subunit XLɑs. Calcified tissue international 3 32596800
2020 Development of Conformational Antibodies to Detect Bcl-xL's Amyloid Aggregates in Metal-Induced Apoptotic Neuroblastoma Cells. International journal of molecular sciences 3 33076337
2025 PAXX/Ku interaction is rate limiting for repair of double-strand DNA breaks requiring end processing. The Journal of biological chemistry 1 40659092
2020 Corrigendum to: Robust DNA repair in PAXX-deficient mammalian cells. FEBS open bio 0 32025478

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