DDA1 (DET1- and DDB1-associated protein 1) is a small, evolutionarily conserved subunit shared by numerous CUL4-RING (CRL4) E3 ubiquitin ligase complexes. It is an integral, core component of DCX/CRL4 complexes built on a core of DDB1, cullin-4 (CUL4A or CUL4B) and RBX1, where it functions as a scaffolding subunit that wraps around DDB1 and the substrate receptor (DCAF) to stabilize the assembled ligase and promote efficient, processive substrate ubiquitination. DDA1 is not itself a substrate receptor and does not provide the catalytic RING; rather it acts as an accessory/stabilizing module that rigidifies the complex and positions the substrate for ubiquitin transfer. It engages DDB1 with high affinity (Kd in the low-nanomolar range) through a conserved extreme N-terminal segment (approximately the first 28 residues) that docks into a groove on the BPA beta-propeller of DDB1, anchoring DDA1 within the assembled ligase. It has been structurally and biochemically characterized as part of the DDB1-DCAF15-DDA1 ligase that mediates aryl-sulfonamide (indisulam/E7820)-induced neosubstrate degradation of the splicing factor RBM39 (and its paralog RBM23), and it is also part of the DDD core complex (DET1-DDA1-DDB1) that recruits UBE2E-family E2 enzymes. DDA1 is additionally an integral, structurally resolved component of the CRL4(CSA) ligase, where it modestly stabilizes the CSA-DDB1 module and helps coordinate the ubiquitination dynamics that drive transcription-coupled nucleotide excision repair at RNA polymerase II stalled on DNA lesions. Through its presence across many CRL4 complexes DDA1 broadly supports CUL4-dependent protein polyubiquitination and proteasomal degradation, with downstream consequences for diverse substrates and pathways. It localizes to the nucleus where most CRL4 complexes act.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic assignment of DDA1 as part of a CUL4-RING E3 ubiquitin ligase complex, its core role as a shared stabilizing subunit. Reason: Core complex membership; DDA1 is an integral component of numerous DCX/CRL4 ligases; supported experimentally and conserved. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0032434 regulation of proteasomal ubiquitin-dependent protein catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based assignment of involvement in regulating proteasomal ubiquitin-dependent protein catabolism, consistent with DDA1 enhancing CRL4-mediated substrate degradation. Reason: Correct; as a stabilizing subunit DDA1 promotes efficient CRL4-mediated ubiquitination and subsequent proteasomal degradation of substrates. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt which mediate the ubiquitination and subsequent proteasomal degradation of target proteins |
| GO:0005515 protein binding | IPI PMID:20562859 Network organization of the human autophagy system. | KEEP AS NON CORE | Summary: Interaction with DDB1 (Q16531) from an autophagy-system interactome study. Bare protein binding is uninformative. Reason: Real DDB1 interaction (core complex partner) but bare protein binding is uninformative; captured by complex membership. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt which consist of a core of DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | KEEP AS NON CORE | Summary: Interactions (Q6RW13, Q96DZ9/DCAF15) from a proteome-scale interactome study. Bare protein binding is uninformative. Reason: High-throughput interactions including DCAF15 (a CRL4 substrate receptor DDA1 stabilizes), but bare protein binding is uninformative. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Component of the DCX(DCAF15) complex, also named CLR4(DCAF15) complex, composed of DCAF15, DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1 |
| GO:0005515 protein binding | IPI PMID:30564455 Structural insights into DDA1 function as a core component o... | KEEP AS NON CORE | Summary: Interaction with DDB1 (Q16531) from the structural study of DDA1 as a core component of CRL4-DDB1. The DDB1 contact is mediated by a conserved N-terminal segment binding the DDB1 BPA propeller with low-nanomolar affinity. Bare protein binding is uninformative. Reason: Real, functionally central DDB1 interaction underpinning DDA1's scaffolding role, but bare protein binding is uninformative; captured by complex membership. The specific structural mechanism (N-terminal anchor on the DDB1 BPA propeller) is recorded in the falcon findings. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt acts as a scaffolding subunit required to stabilize the complex file:human/DDA1/DDA1-deep-research-falcon.md Shabek et al. mapped DDB1 binding to a conserved **N-terminal 28-aa segment** (DDA1-NT), solved the **DDB1–DDA1-NT crystal structure at ~3.1 Å**, and localized binding to a groove on the **BPA propeller** of DDB1 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | KEEP AS NON CORE | Summary: Interactions (Q8IZV5, Q96DZ9-2/DCAF15 isoform, Q96KN3) from a binary interactome reference map. Bare protein binding is uninformative. Reason: High-throughput interactome; bare protein binding is uninformative. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | KEEP AS NON CORE | Summary: Interaction (O60260-5, PARK2/parkin isoform) from a neurodegeneration interactome study. Bare protein binding is uninformative. Reason: High-throughput interactome; bare protein binding is uninformative and not a core function. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | KEEP AS NON CORE | Summary: Interaction with DDB1 (Q16531) from the OpenCell endogenous-tagging interactome. Bare protein binding is uninformative. Reason: Real DDB1 interaction but bare protein binding is uninformative; captured by complex membership. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt which consist of a core of DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1 |
| GO:0016567 protein ubiquitination | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway-derived general protein-ubiquitination process, consistent with DDA1's role in CRL4-mediated ubiquitination. Reason: Correct; DDA1 contributes to CRL4-mediated protein ubiquitination as a stabilizing subunit. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt PATHWAY: Protein modification; protein ubiquitination. |
| GO:0031464 Cul4A-RING E3 ubiquitin ligase complex | IPI PMID:31693891 Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to ... | ACCEPT | Summary: Physical-interaction (ComplexPortal) evidence that DDA1 is part of the CUL4A-RING (CRL4A-DCAF15) ligase complex. Core complex membership. Reason: Core complex membership with experimental support; DDA1 is part of CRL4(DCAF15). Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt composed of DCAF15, DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1 |
| GO:0031465 Cul4B-RING E3 ubiquitin ligase complex | NAS PMID:31452512 Systematic identification of cancer cell vulnerabilities to ... | ACCEPT | Summary: Author statement (ComplexPortal) that DDA1 is part of the CUL4B-RING (CRL4B-DCAF15) ligase complex. Core complex membership. Reason: Core complex membership; DDA1 is a shared subunit of CUL4A- and CUL4B-based CRL4(DCAF15) ligases. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt composed of DCAF15, DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1 |
| GO:0032814 regulation of natural killer cell activation | NAS PMID:31452512 Systematic identification of cancer cell vulnerabilities to ... | KEEP AS NON CORE | Summary: Author statement linking the CRL4-DCAF15 ligase (of which DDA1 is the stabilizing subunit) to regulation of NK-cell-mediated immune surveillance; DCAF15 disruption sensitizes cancer cells to NK clearance. Reason: A real but indirect, context-specific role mediated through the DCAF15 substrate receptor; peripheral to DDA1's core CRL4-stabilizing function. Supporting Evidence: PMID:31452512 the ubiquitin ligase substrate adaptor DCAF15 strongly sensitized cancer cells to NK-mediated clearance |
| GO:0000209 protein polyubiquitination | IMP PMID:31686031 Structural complementarity facilitates E7820-mediated degrad... | ACCEPT | Summary: Mutant-phenotype evidence that DDA1, within the DDB1-DCAF15-DDA1 core ligase, supports polyubiquitination (E7820-mediated RBM39 degradation). Core process role. Reason: Supported; the DDB1-DCAF15-DDA1 ligase polyubiquitinates RBM39, with DDA1 stabilizing the DCAF15 fold. Supporting Evidence: PMID:31686031 We show that DCAF15 adopts a new fold stabilized by DDA1 |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IDA PMID:28302793 Anticancer sulfonamides target splicing by inducing RBM39 de... | ACCEPT | Summary: Direct evidence that DDA1 is part of a CUL4-RING (CRL4-DCAF15) E3 ligase complex mediating RBM39 degradation. Core complex membership. Reason: Core complex membership with direct support. Supporting Evidence: PMID:28302793 indisulam promotes the recruitment of RBM39 (RNA binding motif protein 39) to the CUL4-DCAF15 E3 ubiquitin ligase |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IDA PMID:31686031 Structural complementarity facilitates E7820-mediated degrad... | ACCEPT | Summary: Direct (cryo-EM) evidence that DDA1 is part of the DDB1-DCAF15-DDA1 core CRL4 ligase complex. Core complex membership. Reason: Core complex membership with direct structural support. Supporting Evidence: PMID:31686031 the cryo-EM structure of the DDB1-DCAF15-DDA1 core ligase complex bound to RBM39 |
| GO:0005515 protein binding | IPI PMID:16949367 A family of diverse Cul4-Ddb1-interacting proteins includes ... | KEEP AS NON CORE | Summary: Interactions with DDB1, CUL4A and CUL4B from the DCAF-family study; establishes DDA1 association with the CUL4-DDB1 core. Bare protein binding is uninformative. Reason: Real core-complex interactions but bare protein binding is uninformative; captured by complex membership. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt which consist of a core of DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1 |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IDA PMID:16949367 A family of diverse Cul4-Ddb1-interacting proteins includes ... | ACCEPT | Summary: Direct evidence (DCAF-family study) that DDA1 is part of a CUL4-RING E3 ligase complex. Core complex membership. Reason: Core complex membership with direct support. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8952638 | ACCEPT | Summary: Reactome curation of DDA1 nucleoplasmic localization within a CRL4 neddylation reaction. Consistent with the nuclear site of CRL4 action. Reason: Correct localization; CRL4 complexes containing DDA1 act in the nucleus. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8952639 | ACCEPT | Summary: Reactome curation of DDA1 nucleoplasmic localization within a CRL4 neddylation reaction. Reason: Correct localization; redundant with the other nucleoplasm annotations. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8955245 | ACCEPT | Summary: Reactome curation of DDA1 nucleoplasmic localization within a CRL4 regulation reaction (CAND1 binds CRL4). Reason: Correct localization; redundant with the other nucleoplasm annotations. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8955285 | ACCEPT | Summary: Reactome curation of DDA1 nucleoplasmic localization within a CRL4 regulation reaction (COMMDs displace CAND1). Reason: Correct localization; redundant with the other nucleoplasm annotations. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8956045 | ACCEPT | Summary: Reactome curation of DDA1 nucleoplasmic localization within a CRL4 regulation reaction (COP9 signalosome deneddylates CRL4). Reason: Correct localization; redundant with the other nucleoplasm annotations. Supporting Evidence: file:human/DDA1/DDA1-uniprot.txt Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes |
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Download this section (compressed HTML)Q: Across the full repertoire of CRL4 complexes, which substrate receptors (DCAFs) depend most strongly on DDA1 for assembly/activity, and is DDA1 dispensable for some?
Q: Does DDA1 contribute only to complex stability and substrate positioning, or does it also influence ubiquitin-chain processivity, linkage type, or neddylation/deneddylation dynamics of CRL4 ligases?
Q: In CRL4(CSA)-dependent transcription-coupled repair, does DDA1 act primarily by stabilizing the CSA-DDB1 module, by tuning the residence time/ubiquitination progression on lesion-stalled RNA polymerase II, or both, and which TC-NER substrates (e.g., CSB, UVSSA, RNAPII) depend on DDA1 for timely turnover?
Experiment: Compare RBM39 (and endogenous substrate) ubiquitination kinetics in reconstituted DDB1-CUL4-RBX1-DCAF complexes with and without DDA1, measuring effects on substrate affinity, ubiquitin-transfer rate, and processivity.
Experiment: Perform quantitative proteomics of DDA1-knockout versus wild-type cells to define which CRL4 substrate pools are stabilized, distinguishing DDA1-dependent from DDA1-independent CRL4 functions.
Experiment: In DDA1-depleted cells, measure TC-NER kinetics (e.g., recovery of RNA synthesis after UV, RNAPII clearance from lesions, and ubiquitination of CSB/UVSSA) to test whether DDA1 is required for efficient CRL4(CSA)-driven repair progression, and reconstitute CRL4(CSA) in vitro +/- DDA1 to dissect its effect on ubiquitination dynamics.
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