Affinage

DTX3

E3 ubiquitin-protein ligase DTX3 · UniProt Q8N9I9

Length
347 aa
Mass
38.0 kDa
Annotated
2026-06-09
30 papers in source corpus 10 papers cited in narrative 11 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

DTX3 is a RING finger E3 ubiquitin ligase that ubiquitinates a range of protein substrates and thereby restrains oncogenic signaling (PMID:12670957, PMID:31854042). Its canonical activity targets Notch-family proteins for degradation: DTX3 ubiquitinates NOTCH2 (PMID:31854042) and NOTCH4 (PMID:33300431), and binds the Notch intracellular domain (NICD) through its C-terminal RING domain to drive its ubiquitination and proteasomal turnover, suppressing Notch pathway activation (PMID:40127622). Beyond Notch, DTX3 ubiquitinates XRCC5 (Ku80) in the nucleus to inhibit AKT signaling (PMID:33403043), and stabilizes mutant p53 by perturbing the MDM2–mutant p53 interaction, illustrating that its ubiquitination output is not uniformly degradative (PMID:35782979). Across these contexts DTX3 generally acts as a tumor suppressor, with overexpression reducing proliferation, migration, and invasion (PMID:31854042, PMID:40127622). DTX3 also catalyzes non-canonical ubiquitylation: it directly modifies DNA and RNA in vitro via ester-bond formation with preference for 3'-terminal adenosine (PMID:39242775). A novel N-terminal isoform, DTX3c, assembles with UBA1, UBE2N and the Cdc48/p97 ATPase to ubiquitinate EphB4 upon IGF-II deprivation (PMID:37108544). DTX3 family members homo- and heterodimerize, modulating E3 activity and substrate availability (PMID:12670957), and DTX3 mRNA is itself destabilized by the RNA-binding protein DCAF13, which acts on a 3'UTR AU-rich element (PMID:33300431).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2003 High

    Established DTX3 as a catalytically active E3 ligase and revealed that DTX family members physically associate to modulate one another's activity, framing DTX3 within a regulatable ligase network.

    Evidence In vitro self-ubiquitination assay, yeast two-hybrid, and Co-IP demonstrating dimerization

    PMID:12670957

    Open questions at the time
    • No physiological substrate identified at this stage
    • Functional consequence of dimerization on specific targets not defined
  2. 2020 Medium

    Identified Notch receptors as DTX3 substrates, defining a degradative axis that links DTX3 to suppression of Notch-driven tumor phenotypes.

    Evidence Y2H, ubiquitination assays, and gain/loss-of-function in esophageal carcinoma (NOTCH2) and triple-negative breast cancer (NOTCH4)

    PMID:31854042 PMID:33300431

    Open questions at the time
    • Ubiquitin chain topology not defined
    • Direct vs indirect ubiquitination of receptor not fully resolved
  3. 2020 Medium

    Showed DTX3 itself is post-transcriptionally controlled, placing it downstream of an RNA-decay pathway that derepresses Notch signaling when DTX3 is lost.

    Evidence RBP-ARE binding and mRNA stability assays for DCAF13 in triple-negative breast cancer

    PMID:33300431

    Open questions at the time
    • Upstream regulators of DCAF13 not addressed
    • Generality of this control across tissues unknown
  4. 2020 Medium

    Demonstrated that DTX3 ubiquitination can stabilize rather than degrade a substrate, by acting on mutant p53 and perturbing MDM2 engagement.

    Evidence Reciprocal Co-IP, ubiquitination assay, and in vitro/in vivo functional assays in ovarian carcinoma

    PMID:35782979

    Open questions at the time
    • Ubiquitin linkage type producing stabilization not characterized
    • Whether wild-type p53 is similarly affected unclear
  5. 2021 Medium

    Extended DTX3 substrates to nuclear XRCC5 (Ku80) and connected its ligase activity to AKT-driven EMT suppression.

    Evidence IP-MS, Co-IP, immunofluorescence co-localization, and ubiquitination assay in papillary thyroid carcinoma

    PMID:33403043

    Open questions at the time
    • Mechanistic link between XRCC5 ubiquitination and AKT signaling not detailed
    • Fate of ubiquitinated XRCC5 not established
  6. 2022 Low

    Linked DTX3 to E2F1 transcriptional output and cell-cycle gene expression in colorectal cancer, though without a direct biochemical connection.

    Evidence Overexpression/knockout with proliferation, colony formation, and E2F1 target readouts

    PMID:35098394

    Open questions at the time
    • No direct DTX3–E2F1 interaction demonstrated
    • Whether the effect is ligase-dependent unknown
  7. 2023 Medium

    Defined a DTX3c isoform-specific ubiquitination machine coupling DTX3 to the p97 ATPase and growth-factor signaling for EphB4 turnover.

    Evidence Targeted proteomics, Co-IP, isoform cloning, and 3D modeling identifying UBA1/UBE2N/Cdc48-p97 complex

    PMID:37108544

    Open questions at the time
    • Physiological scope of DTX3c beyond EphB4 unknown
    • Direct ubiquitin transfer reconstitution not shown
  8. 2024 High

    Revealed a non-protein activity, establishing that DTX3 ubiquitylates nucleic acids via reversible ester bonds with sequence preference.

    Evidence In vitro reconstitution with purified components, ester-bond characterization, and DUB reversal assays

    PMID:39242775

    Open questions at the time
    • Cellular substrates and biological role of nucleic acid ubiquitylation unknown
    • Targeting/specificity determinants in cells undefined
  9. 2025 Medium

    Showed DTX3 writes a non-canonical ubiquitin-on-MAR hybrid mark on tankyrase that protects it from RNF146-mediated degradation, expanding DTX3 chemistry to ADP-ribose acceptors.

    Evidence Cell-based ubiquitylation assays, ubiquitin-MAR linkage characterization, and genetic epistasis with RNF146/RNF114/RNF166 (preprint)

    PMID:bio_10.1101_2025.04.09.648013

    Open questions at the time
    • Not yet peer-reviewed
    • Broader substrate range of the MAR-ubiquitin mark unknown
  10. 2025 Medium

    Confirmed direct NICD binding through the DTX3 RING domain, mapping the structural basis for Notch suppression and metastasis control.

    Evidence Co-IP, domain mapping, ubiquitination assay, and migration/invasion assays with DAPT epistasis in bladder cancer

    PMID:40127622

    Open questions at the time
    • Ubiquitin chain type on NICD not defined
    • Relative contribution of NICD vs full-length receptor ubiquitination unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • How DTX3 selects between degradative and stabilizing outcomes, and what governs its choice among protein, nucleic acid, and ADP-ribose acceptors in vivo, remains unresolved.
  • No unifying model for substrate/linkage selectivity
  • In vivo relevance of nucleic acid and MAR ubiquitylation not established
  • Structural basis of multi-acceptor catalysis unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 9 GO:0140096 catalytic activity, acting on a protein 6 GO:0016874 ligase activity 3 GO:0003677 DNA binding 1 GO:0003723 RNA binding 1
Localization
GO:0005634 nucleus 1
Pathway
R-HSA-392499 Metabolism of proteins 7 R-HSA-1643685 Disease 5 R-HSA-162582 Signal Transduction 4
Partners
DCAF13EPHB4NOTCH2NOTCH4TP53UBA1UBE2NXRCC5

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2003 DTX3, like other DTX family members (DTX1, DTX2), functions as an E3 ubiquitin-protein isopeptide ligase, demonstrated by its capacity for self-ubiquitination in vitro. DTX family members homodimerize and heterodimerize in vivo, and physical interactions between DTX family members modify E3 activity and/or substrate availability. In vitro self-ubiquitination assay, yeast two-hybrid screen, co-immunoprecipitation The Journal of biological chemistry High 12670957
2020 DTX3 ubiquitinates NOTCH2, promoting its degradation. DTX3 overexpression suppressed proliferation and tumorigenicity of esophageal carcinoma cells, and DTX3 was identified as a novel E3 ligase for NOTCH2 by yeast two-hybrid screening. Yeast two-hybrid screening, ubiquitination assay, overexpression/knockdown with cell proliferation and migration readouts Cancer science Medium 31854042
2020 DCAF13 binds the AU-rich element (ARE) in the DTX3 mRNA 3'UTR and accelerates its degradation, acting as an RNA-binding protein. Reduced DTX3 levels consequently activate NOTCH4 signaling in triple-negative breast cancer. RNA-binding protein assay (RBP-ARE interaction), mRNA stability assay, overexpression/knockdown with signaling readouts Cell cycle (Georgetown, Tex.) Medium 33300431
2020 DTX3 promotes ubiquitination and proteasomal degradation of NOTCH4 in triple-negative breast cancer cells. Ubiquitination assay, overexpression/knockdown with western blot for NOTCH4 protein levels Cell cycle (Georgetown, Tex.) Medium 33300431
2020 DTX3 interacts with mutant p53 in ovarian carcinoma cells, mediates its ubiquitination and stabilization by perturbing the MDM2-mutant p53 interaction, and consequently activates mutant p53 target genes. DTX3 depletion suppressed ovarian cancer cell proliferation and invasion in a mutant p53-dependent manner. Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown with cell proliferation, invasion, and in vivo tumor growth assays Genes & diseases Medium 35782979
2021 DTX3 co-localizes with XRCC5 (Ku80) in the nucleus, promotes its ubiquitination, and inhibits AKT signaling, thereby suppressing epithelial-mesenchymal transition in papillary thyroid carcinoma cells. IP-mass spectrometry, co-immunoprecipitation, immunofluorescence co-localization, ubiquitination assay, overexpression/knockdown with EMT and AKT signaling readouts Journal of Cancer Medium 33403043
2022 DTX3 overexpression reduced E2F1 transcriptional activity and downstream target gene expression (CDC2, Cyclin D3), inhibiting CRC cell proliferation and colony formation, while DTX3 knockout had the opposite effect. Overexpression/knockout with cell proliferation, colony formation assays; transcriptional reporter/western blot for E2F1 target genes Molecular biology reports Low 35098394
2024 DTX3 (like DTX3L, but not DTX1, DTX2, or DTX4) directly ubiquitylates DNA and RNA in vitro via ester bond formation, with preference for 3'-terminal adenosine. This nucleic acid ubiquitylation is reversible by deubiquitylases USP2, JOSD1, and SARS-CoV-2 PLpro. In vitro ubiquitylation assay with purified components, biochemical characterization of ester-bond linkage, DUB reversal assay EMBO reports High 39242775
2023 A novel N-terminal isoform of DTX3 (DTX3c) associates with UBA1 (E1), UBE2N (E2), and Cdc48/p97 ATPase as part of a complex that ubiquitinates EphB4 kinase at its C-tail upon IGF-II signal deprivation, promoting EphB4 degradation. Cdc48/p97 ATPase activity was required for EphB4 recruitment to this complex. Targeted proteomics, co-immunoprecipitation, PCR cloning (isoform identification), 3D modeling International journal of molecular sciences Medium 37108544
2025 DTX3 catalyzes monoubiquitylation of tankyrase in cells, occurring on mono-ADP-ribose (MAR) rather than a canonical lysine, creating a monoubiquitin-MAR hybrid mark. This mark prevents PAR formation on tankyrase, antagonizing RNF146-mediated degradation and thereby stabilizing tankyrase. The hybrid mark is subsequently recognized and extended by RING-UIM E3 ligases RNF114 and RNF166. Cell-based ubiquitylation assays, biochemical characterization of ubiquitin-MAR linkage, genetic epistasis with RNF146/RNF114/RNF166 bioRxivpreprint Medium bio_10.1101_2025.04.09.648013
2025 DTX3 binds to the Notch intracellular domain (NICD) via its C-terminal RING finger domain, promotes NICD ubiquitination and degradation, and thereby suppresses Notch pathway activation, inhibiting bladder cancer cell migration and invasion. The Notch inhibitor DAPT partially reversed the effects of DTX3 knockdown on metastatic ability. Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown with migration/invasion assays in vitro and in vivo; domain mapping International immunopharmacology Medium 40127622

Source papers

Stage 0 corpus · 30 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer. Nature genetics 213 25151356
2003 The BAL-binding protein BBAP and related Deltex family members exhibit ubiquitin-protein isopeptide ligase activity. The Journal of biological chemistry 127 12670957
2010 Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer. BMC molecular biology 70 20122155
2021 Functions and Molecular Mechanisms of Deltex Family Ubiquitin E3 Ligases in Development and Disease. Frontiers in cell and developmental biology 44 34513839
2019 Multi-species okadaic acid contamination and human poisoning during a massive bloom of Dinophysis acuminata complex in southern Brazil. Harmful algae 41 31672229
2005 Metabolic transformation of dinophysistoxin-3 into dinophysistoxin-1 causes human intoxication by consumption of O-acyl-derivatives dinophysistoxins contaminated shellfish. The Journal of toxicological sciences 40 16404137
2013 In vitro acylation of okadaic acid in the presence of various bivalves' extracts. Marine drugs 30 23434830
2020 DCAF13 promotes triple-negative breast cancer metastasis by mediating DTX3 mRNA degradation. Cell cycle (Georgetown, Tex.) 28 33300431
2021 Highly sensitive electrochemical detection of the marine toxins okadaic acid and domoic acid with carbon black modified screen printed electrodes. Talanta 27 33773701
2020 Ubiquitination of NOTCH2 by DTX3 suppresses the proliferation and migration of human esophageal carcinoma. Cancer science 27 31854042
2024 Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L. EMBO reports 20 39242775
2015 Assimilation, Accumulation, and Metabolism of Dinophysistoxins (DTXs) and Pectenotoxins (PTXs) in the Several Tissues of Japanese Scallop Patinopecten yessoensis. Toxins 20 26633503
2012 Isolation and characterization of an enzyme from the Greenshell™ mussel Perna canaliculus that hydrolyses pectenotoxins and esters of okadaic acid. Toxicon : official journal of the International Society on Toxinology 17 22613166
2023 The DTX Protein Family: An Emerging Set of E3 Ubiquitin Ligases in Cancer. Cells 14 37443713
2021 Deltex3 inhibits Epithelial Mesenchymal Transition in Papillary Thyroid Carcinoma via promoting ubiquitination of XRCC5 to regulate the AKT signal pathway. Journal of Cancer 14 33403043
2021 Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis. PeerJ 14 33987007
2022 Genome-wide analysis of genes encoding core components of the ubiquitin system during cerebral cortex development. Molecular brain 11 35974412
2010 First evidence of Okadaic acid acyl-derivative and Dinophysistoxin-3 in mussel samples collected in Chiloe Island, Southern Chile. The Journal of toxicological sciences 11 20519842
2003 Quantitation of diarrhetic shellfish poisoning toxins in Chilean mussel using pyrenyldiazomethane as fluorescent labeling reagent. Biological research 11 14513712
2020 Ubiquitin ligase DTX3 empowers mutant p53 to promote ovarian cancer development. Genes & diseases 9 35782979
2016 Effect of carbon chain length in acyl coenzyme A on the efficiency of enzymatic transformation of okadaic acid to 7-O-acyl okadaic acid. Bioorganic & medicinal chemistry letters 7 27231127
2022 Deltex E3 ubiquitin ligase 3 inhibits colorectal cancer cell growth and regulates cell cycle progression via upregulating E2F transcription factor 1. Molecular biology reports 6 35098394
2024 The Role of NOTCH Pathway Genes in the Inherited Susceptibility to Aortic Stenosis. Journal of cardiovascular development and disease 5 39057646
2023 Novel Isoform DTX3c Associates with UBE2N-UBA1 and Cdc48/p97 as Part of the EphB4 Degradation Complex Regulated by the Autocrine IGF-II/IRA Signal in Malignant Mesothelioma. International journal of molecular sciences 5 37108544
2021 Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma. Frontiers in genetics 5 34163522
2025 DTX3 suppresses bladder cancer cell invasion and metastasis by inhibiting the Notch signaling pathway. International immunopharmacology 3 40127622
2024 Autophagy-related molecular clusters identified as indicators for distinguishing active and latent TB infection in pediatric patients. BMC pediatrics 3 38890657
2024 Assay for okadaic acid O-acyl transferase using HPLC-FLD. Bioscience, biotechnology, and biochemistry 2 38886126
2025 Hepatocyte reporter cells and integrated metabolomic and transcriptomic analyses reveal insights into hepatocyte changes in offspring of pregnancies with obesity. Scientific reports 0 40715324
2025 DTX3 inhibits cell migration, invasion, and epithelial-mesenchymal transition in colorectal cancer through the AKT signaling pathway. Translational cancer research 0 41158261

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