Affinage

HERC3

Probable E3 ubiquitin-protein ligase HERC3 · UniProt Q15034

Length
1050 aa
Mass
117.2 kDa
Annotated
2026-06-10
12 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

HERC3 is a HECT-domain E3 ubiquitin ligase that functions as a hub for targeted proteasomal protein degradation, controlling signaling pathways that govern proliferation, senescence, epithelial-mesenchymal transition, and protein quality control (PMID:26476452, PMID:35637966). Through its HECT domain it catalyzes K48-linked (and in some substrates K27-linked) polyubiquitination of multiple targets—including MM1 in a ΔNp63α→HERC3→MM1→c-Myc senescence axis (PMID:29880857), the eukaryotic translation factor EIF5A2 (PMID:35064108), the ribosomal protein RPL23A acting on the c-Myc/p21 axis to arrest cells at G0/G1 (PMID:35637966), and NCOA1 to restrain a NCOA1-p300-Runx2 complex that drives matrix metalloproteinase expression (PMID:36878279); substrate engagement can occur through its RCC1 domain, as shown for EIF5A2 (PMID:35064108). HERC3 also drives degradation of SMAD7 in an autolysosome-dependent manner, relieving inhibition of TGFβ/SMAD2/3 signaling and promoting EMT (PMID:30862693). Notably, a subset of HERC3's regulatory functions is independent of its catalytic ligase activity: it restrains NF-κB by bridging liberated RelA to the 26S proteasome together with UBQLN1 (PMID:26476452), and it stabilizes YAP/TAZ by directly binding β-TrCP to block adaptor access (PMID:36598329). In ER-associated degradation, HERC3 defines a distinct branch that recognizes exposed cytoplasmic membrane-spanning domains of misfolded membrane proteins such as CFTR, operating independently of the ER-embedded ligases RNF5 and RNF185 (PMID:38722278). In vivo, loss of HERC3 in mice causes subretinal microglial activation and retinal degeneration, establishing a non-redundant homeostatic role (PMID:38321224).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2001 Medium

    Established HERC3 as a cytosolic/vesicular HECT-family protein that non-covalently binds ubiquitin and is itself a proteasome substrate, framing its biology around the ubiquitin system before any substrate was known.

    Evidence Subcellular fractionation, immunofluorescence co-localization with β-COP/ARF/Rab5, Co-IP, catalytic-cysteine mutagenesis, and proteasome inhibition

    PMID:11163799

    Open questions at the time
    • No physiological substrate identified
    • Functional consequence of vesicular localization untested
    • Ubiquitin-binding interface not mapped
  2. 2015 High

    Showed HERC3 negatively regulates NF-κB by bridging RelA to the proteasome via UBQLN1, and that this activity is independent of its catalytic ligase function, revealing a scaffolding mode of action.

    Evidence Co-IP, ubiquitination assays, catalytic-dead mutant, NF-κB reporter, nuclear fractionation, and DNA-binding assays

    PMID:26476452

    Open questions at the time
    • Indirect RelA binding partner not fully defined
    • Whether the same complex regulates other transcription factors unknown
  3. 2018 Medium

    Placed HERC3 in a senescence-controlling axis by demonstrating it is transcriptionally induced by ΔNp63α and degrades MM1 via K48-linked ubiquitination to modulate c-Myc.

    Evidence Co-IP, ubiquitination assays, siRNA knockdown, overexpression, and epistasis/senescence assays

    PMID:29880857

    Open questions at the time
    • Direct vs. indirect MM1 binding not resolved
    • Ubiquitination sites on MM1 not mapped
  4. 2019 Medium

    Connected HERC3 to TGFβ/EMT by showing autophagy-induced HERC3 degrades SMAD7 in an autolysosome-dependent manner, enhancing SMAD2/3 signaling.

    Evidence iTRAQ proteomics, Co-IP, ubiquitination assays, knockdown/overexpression, and intracranial xenograft with tissue analysis

    PMID:30862693

    Open questions at the time
    • Mechanism linking ubiquitination to autolysosomal rather than proteasomal degradation unclear
    • Ubiquitin linkage type on SMAD7 not defined
  5. 2022 Medium

    Defined direct substrates and degradation chemistry: HERC3 binds EIF5A2 via its RCC1 domain to drive K27/K48 ubiquitination, and binds RPL23A to drive K48 ubiquitination, linking these to TGFβ/EMT suppression and c-Myc/p21-dependent cell-cycle arrest respectively.

    Evidence Reciprocal Co-IP, GST-pulldown, domain-deletion mutants, MS-based ubiquitination site mapping, cycloheximide chase, and rescue experiments

    PMID:35064108 PMID:35637966

    Open questions at the time
    • Context determining anti- vs. pro-EMT outcomes across substrates unresolved
    • In vitro reconstitution of ligase activity not performed
  6. 2022 Low

    Proposed ERK2 as a HERC3 substrate linked to p53-mediated apoptosis, extending HERC3 into MAPK signaling.

    Evidence Co-IP, GST-pulldown, ubiquitination assays, and xenograft model

    PMID:35889210

    Open questions at the time
    • Single low-confidence study with limited mechanistic detail on ubiquitination
    • Ubiquitin linkage and sites on ERK2 not defined
    • p53 link correlative
  7. 2023 High

    Demonstrated a ligase-independent stabilizing function in which HERC3 binds β-TrCP to block YAP/TAZ ubiquitination, driving Hippo-independent tumorigenesis.

    Evidence Reciprocal Co-IP, catalytic-dead mutant, ubiquitination/protein-stability assays, knockdown, and breast tumor tissue correlation

    PMID:36598329

    Open questions at the time
    • Structural basis of β-TrCP competition unknown
    • Whether HERC3 blocks other β-TrCP substrates untested
  8. 2023 Medium

    Identified NCOA1 as a HERC3 substrate whose loss derepresses a NCOA1-p300-Runx2 transcriptional complex driving MMP-mediated matrix degradation in disc degeneration.

    Evidence Co-IP/MS, ubiquitination assays, HERC3-deficient model, and aged mouse IDD model

    PMID:36878279

    Open questions at the time
    • Ubiquitin linkage and sites on NCOA1 not mapped
    • Direct vs. indirect engagement not fully resolved
  9. 2024 High

    Defined a distinct ERAD branch in which HERC3 directly recognizes exposed cytoplasmic membrane-spanning domains of misfolded CFTR, acting independently of ER-embedded ligases RNF5/RNF185.

    Evidence Multiplex KD/KO, real-time kinetic ERAD assays, in vitro binding to liposome-embedded vs. exposed MSDs, and CFTR/ABCB1 substrate models

    PMID:38722278

    Open questions at the time
    • Structural determinants of MSD recognition unresolved
    • Full substrate repertoire of this ERAD branch unknown
  10. 2024 Medium

    Established a non-redundant in vivo role for HERC3 in retinal homeostasis, with knockout causing subretinal microglial activation and retinal degeneration.

    Evidence CRISPR knockout mice with fundus imaging, OCT, histology, optomotor testing, electrophysiology, and bulk RNA-seq

    PMID:38321224

    Open questions at the time
    • Causal substrate driving the retinal phenotype not identified
    • Cell-autonomous vs. non-autonomous microglial effects unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unknown how HERC3 selects between catalytic degradation and ligase-independent scaffolding modes, and which substrate(s) account for its in vivo developmental and homeostatic phenotypes.
  • No unifying model for substrate recognition across diverse targets
  • No structural data on HECT/RCC1 substrate engagement
  • In vivo substrate(s) linking molecular activity to organismal phenotype undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0016874 ligase activity 2 GO:0060090 molecular adaptor activity 2
Localization
GO:0005783 endoplasmic reticulum 1 GO:0005829 cytosol 1 GO:0031410 cytoplasmic vesicle 1
Pathway
R-HSA-392499 Metabolism of proteins 4 R-HSA-162582 Signal Transduction 3 R-HSA-1640170 Cell Cycle 1
Partners
BTRCCFTREIF5A2MAPK1NCOA1RELARPL23AUBQLN1
Complex memberships
RelA-UBQLN1-26S proteasome complex

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 HERC3 protein localizes to the cytosol and vesicular-like structures containing β-COP, ARF, and Rab5, suggesting a role in vesicular trafficking. HERC3 non-covalently binds ubiquitin, and this binding does not require the conserved catalytic cysteine in the HECT domain. HERC3 itself is a substrate of ubiquitination and is degraded by the proteasome. Subcellular fractionation, immunofluorescence co-localization, co-immunoprecipitation, mutagenesis of catalytic cysteine, proteasome inhibitor treatment FEBS letters Medium 11163799
2015 HERC3 acts as a negative regulator of NF-κB by binding (indirectly) to the RelA subunit after its liberation from IκBα, facilitating RelA ubiquitination and proteasomal degradation. HERC3 restricts NF-κB nuclear import and DNA binding without affecting IκBα degradation. Remarkably, this regulatory activity is independent of HERC3's intrinsic E3 ubiquitin ligase activity. HERC3, RelA, ubiquilin-1 (UBQLN1), and the 26S proteasome form a multi-protein complex, and HERC3/UBQLN1 provide a bridge between RelA and the proteasome. Co-immunoprecipitation, ubiquitination assays, catalytic-dead mutant analysis, NF-κB reporter assays, nuclear fractionation, DNA-binding assays Nucleic acids research High 26476452
2018 ΔNp63α transcriptionally upregulates HERC3, and HERC3 then mediates K48-linked ubiquitination and proteasomal degradation of MM1 (a c-Myc modulator). Knockdown of HERC3 abrogates ΔNp63α-induced MM1 downregulation and induces cell senescence, placing HERC3 in a ΔNp63α→HERC3→MM1→c-Myc axis controlling cell senescence. Co-immunoprecipitation, ubiquitination assays, siRNA knockdown, overexpression, reporter/senescence assays, epistasis experiments Cell death and differentiation Medium 29880857
2019 HERC3 promotes ubiquitination-mediated degradation of SMAD7 in an autolysosome-dependent manner. This leads to increased p-SMAD2/3 levels and TGFβ pathway activation, driving EMT. Autophagy inducers upregulate HERC3 expression, establishing a mechanistic link between autophagy and TGFβ/SMAD signaling via HERC3-mediated SMAD7 degradation. iTRAQ proteomics, co-immunoprecipitation, ubiquitination assays, siRNA/overexpression, intracranial xenograft, immunohistochemistry, tissue microarray Clinical cancer research Medium 30862693
2022 HERC3 directly interacts with EIF5A2 via its RCC1 domain and promotes K27- and K48-linked ubiquitination degradation of EIF5A2 via its HECT domain. Specific ubiquitination sites on EIF5A2 were identified as K47, K67, K85, and K121. This interaction inhibits EMT and metastasis in colorectal cancer through the EIF5A2/TGFβ/Smad2/3 signaling axis. Co-immunoprecipitation, GST-pulldown, in vivo ubiquitination assays, domain-deletion mutants, transwell/wound healing assays, mass spectrometry Cell death & disease Medium 35064108
2022 HERC3 directly interacts with RPL23A and acts as an E3 ligase to ubiquitinate and degrade RPL23A via K48-linked polyubiquitination through its HECT domain. HERC3-mediated RPL23A degradation modulates the c-Myc/p21 axis and regulates CRC cell proliferation and cell-cycle arrest at G0/G1. Co-immunoprecipitation, mass spectrometry, GST-pulldown, in vivo ubiquitination assays, cycloheximide chase, loss/gain-of-function experiments, rescue experiments International journal of biological sciences Medium 35637966
2022 HERC3 directly interacts with ERK2 through its HECT domain and promotes ERK2 ubiquitination. HERC3 also modulates p53 protein levels and phosphorylation, linking ERK2 degradation to p53-mediated apoptosis. Co-immunoprecipitation, GST-pulldown, ubiquitination assays, xenograft model Molecules Low 35889210
2023 HERC3 promotes YAP/TAZ protein stability and Hippo-independent tumorigenesis independently of its E3 ubiquitin ligase enzymatic activity. HERC3 directly binds to β-TrCP (the YAP/TAZ ubiquitin E3 ligase adaptor), blocking β-TrCP interaction with YAP/TAZ and thereby preventing YAP/TAZ ubiquitination and proteasomal degradation. Co-immunoprecipitation, catalytic-dead mutant analysis, ubiquitination assays, knockdown, protein stability assays, breast tumor cell/tissue correlation The EMBO journal High 36598329
2023 HERC3 ubiquitinates NCOA1, targeting it for proteasomal degradation. HERC3 deficiency leads to NCOA1 accumulation, which assembles a NCOA1-p300-Runx2 complex that transactivates matrix metallopeptidase (MMP) gene expression, promoting extracellular matrix degradation in intervertebral disc degeneration. Immunoprecipitation, mass spectrometry, ubiquitination assays, loss-of-function (HERC3-deficient model), immunoblot, aged mouse IDD model Life sciences Medium 36878279
2024 HERC3 facilitates ERAD of select membrane proteins by directly recognizing exposed (cytoplasmic) membrane-spanning domains (MSDs) of misfolded CFTR, but not MSDs embedded in liposomes. HERC3 operates independently of the ER-embedded E3 ligases RNF5 and RNF185 to mediate retrotranslocation and ERAD of misfolded CFTR. This identifies a distinct ERAD branch for cytoplasmic quality control of membrane-spanning domains. Multiplex knockdown/knockout experiments, real-time kinetic ERAD assays, in vitro binding assay with liposome-embedded vs. exposed MSDs, CFTR/ABCB1 misfolded substrate models The Journal of cell biology High 38722278
2024 CRISPR-generated Herc3-/- mice develop accumulation of activated subretinal microglia (Iba1+/CD16+), retinal thinning, and functional deficits, demonstrating a non-redundant role for HERC3 in retinal homeostasis and microglial activation suppression in vivo. CRISPR knockout mouse generation, fundus imaging, OCT, histology, optomotor testing, electrophysiology, bulk RNA sequencing Scientific reports Medium 38321224

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2019 HERC3-Mediated SMAD7 Ubiquitination Degradation Promotes Autophagy-Induced EMT and Chemoresistance in Glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research 89 30862693
2012 Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic acids research 40 22790983
2001 HERC3 binding to and regulation by ubiquitin. FEBS letters 34 11163799
2015 The ubiquitin ligase HERC3 attenuates NF-κB-dependent transcription independently of its enzymatic activity by delivering the RelA subunit for degradation. Nucleic acids research 30 26476452
2022 HERC3 regulates epithelial-mesenchymal transition by directly ubiquitination degradation EIF5A2 and inhibits metastasis of colorectal cancer. Cell death & disease 28 35064108
2018 ΔNp63α down-regulates c-Myc modulator MM1 via E3 ligase HERC3 in the regulation of cell senescence. Cell death and differentiation 28 29880857
2023 HERC3 promotes YAP/TAZ stability and tumorigenesis independently of its ubiquitin ligase activity. The EMBO journal 24 36598329
2022 HERC3 directly targets RPL23A for ubiquitination degradation and further regulates Colorectal Cancer proliferation and the cell cycle. International journal of biological sciences 17 35637966
2024 HERC3 facilitates ERAD of select membrane proteins by recognizing membrane-spanning domains. The Journal of cell biology 10 38722278
2023 Accumulation of NCOA1 dependent on HERC3 deficiency transactivates matrix metallopeptidases and promotes extracellular matrix degradation in intervertebral disc degeneration. Life sciences 10 36878279
2024 E3 ubiquitin ligase Herc3 deficiency leads to accumulation of subretinal microglia and retinal neurodegeneration. Scientific reports 7 38321224
2022 A Novel ERK2 Degrader Z734 Induces Apoptosis of MCF-7 Cells via the HERC3/p53 Signaling Pathway. Molecules (Basel, Switzerland) 1 35889210

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