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Showing MYCBP2PHR1 is a alias.

MYCBP2

E3 ubiquitin-protein ligase MYCBP2 · UniProt O75592

Length
4678 aa
Mass
513.6 kDa
Annotated
2026-06-10
24 papers in source corpus 16 papers cited in narrative 18 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

MYCBP2 is a large atypical RING-type E3 ubiquitin ligase that functions as a substrate-selective hub within multi-protein complexes to control mitotic cell fate, neuronal development and signaling, ciliogenesis, and metabolic regulation (PMID:31285543, PMID:41052634, PMID:36200388). It partners with distinct specificity factors to direct ubiquitination: with FBXO45 it ubiquitinates and degrades the tumor suppressor FBXW7 during prolonged mitotic arrest to promote mitotic slippage (PMID:31285543), and with the alternative specificity factor SPRYD3 it carries out non-canonical cysteine ubiquitination of the deubiquitinase USP11 at Cys318 to support bipolar spindle formation and slippage under microtubule-targeting drug treatment (PMID:41052634). Its catalytic activity is regulated: SUMOylated RanGAP1 binds MYCBP2 and inhibits its ligase activity, while RGS12 association enhances MYCBP2 phosphorylation to activate it (PMID:26304119, PMID:36700049). Through targeted degradation MYCBP2 controls diverse substrates including KIF2A (promoting ciliogenesis and macrophage/synovial fibroblast phenotypes) (PMID:36700049, PMID:36797232), HNF4α via K33/K48 polyubiquitin chains in lipid metabolism (PMID:40181155), S100A9 in microglia (PMID:38896802), and KIF14 in leukemic cells (PMID:42036047). In neurons it additionally acts independently of degradation, stabilizing the EPHB2 receptor to support ephrin signaling and functioning as a cytoplasmic GEF for the Ran GTPase via its RCC1-like domain (PMID:38289221, PMID:26304119). Loss-of-function variants in MYCBP2 cause a neurodevelopmental disorder (MDCD) with corpus callosum defects, developmental delay, and epilepsy, with loss of ubiquitin ligase activity established as the pathogenic mechanism (PMID:36200388).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 2010 High

    Established that MYCBP2 acts in sensory neurons to restrain p38 MAPK signaling and thereby permit TRPV1 internalization, linking the ligase to nociceptor desensitization.

    Evidence Conditional knockout mouse, p38 MAPK inhibitor rescue, calcium imaging and behavioral assays

    PMID:21098484

    Open questions at the time
    • Direct ubiquitination substrate in the p38/TRPV1 axis not identified
    • Whether MYCBP2 acts on p38 components directly or indirectly unresolved
  2. 2010 High

    Defined the structural fold of the MYCBP2 PHR domains and rationalized a conserved loss-of-function ortholog mutation, providing a structural basis for the protein's function.

    Evidence X-ray crystallography of mouse Mycbp2 PHR1 and PHR2 domains

    PMID:20156452

    Open questions at the time
    • Functional partners bound by the PHR surface loops not defined
    • No structure of the catalytic ligase region
  3. 2013 Medium

    Placed MYCBP2 in an axon-guidance pathway through genetic interaction with Robo2, showing it regulates Robo2 expression in olfactory sensory neurons.

    Evidence Double-heterozygous mouse genetic epistasis and immunohistochemistry

    PMID:23525682

    Open questions at the time
    • Whether Robo2 is a direct ubiquitination substrate not shown
    • Single-lab anatomical phenotype
  4. 2015 Medium

    Revealed a non-ligase enzymatic role: MYCBP2 acts as a Ran GEF via its RCC1-like domain, and its ligase activity is reciprocally inhibited by SUMOylated RanGAP1.

    Evidence Co-IP, GDP/GTP exchange assay, subcellular fractionation in DRG neurons

    PMID:26304119

    Open questions at the time
    • Physiological consequences of Ran GEF activity in neurons incompletely defined
    • Single lab; GEF activity not structurally mapped
  5. 2019 High

    Identified the FBXO45-MYCBP2 ligase complex as a regulator of mitotic cell fate by degrading FBXW7 during mitotic arrest to promote slippage over death.

    Evidence Reciprocal Co-IP, ubiquitylation assays, proteasome rescue, cell fate readouts

    PMID:31285543

    Open questions at the time
    • Upstream signal triggering FBXO45-FBXW7 recognition during arrest unclear
    • In vivo relevance not addressed
  6. 2022 Medium

    Showed RGS12 activates MYCBP2 by enhancing its phosphorylation, driving KIF2A degradation to control ciliogenesis across synovial fibroblasts and endothelial cells in inflammatory arthritis.

    Evidence LC-MS/MS, Co-IP, ubiquitination assays, cilia imaging, RGS12-deficient mouse models

    PMID:36700049 PMID:37193553

    Open questions at the time
    • Kinase phosphorylating MYCBP2 downstream of RGS12 not identified
    • Single-lab findings
  7. 2023 Medium

    Extended the RGS12-MYCBP2-KIF2A axis to macrophage polarization, linking MYCBP2-mediated KIF2A degradation to M1 polarization and antitumor activity.

    Evidence Co-IP, ubiquitination assays, RGS12 knockout macrophages, in vivo tumor models

    PMID:36797232

    Open questions at the time
    • Mechanistic link between KIF2A loss and polarization state incomplete
    • Single lab
  8. 2023 High

    Established a degradation-independent neuronal role: MYCBP2 stabilizes EPHB2 (via FBXO45, kinase-independent, ephrin-destabilized) and is required for efficient EPHB2 signaling.

    Evidence Proteomics screen, reciprocal Co-IP, ubiquitination assays, knockdown in cells and neurons, C. elegans genetics

    PMID:37693478 PMID:38289221

    Open questions at the time
    • Molecular basis for paradoxical stabilization versus the ligase activity unresolved
    • Direct substrate whose degradation protects EPHB2 not identified
  9. 2023 High

    Defined MYCBP2 loss-of-function as the cause of a human neurodevelopmental syndrome (MDCD), with ligase-dead variants causing axon, behavioral, and autophagy defects in a model organism.

    Evidence Exome sequencing of patients, CRISPR variant knock-in in C. elegans, axon imaging, behavior, autophagy marker analysis

    PMID:36200388

    Open questions at the time
    • Mammalian substrates underlying corpus callosum and epilepsy phenotypes not pinned down
    • Genotype-phenotype correlation across variant classes incomplete
  10. 2024 Medium

    Showed MYCBP2 promotes S100A9 degradation in microglia to favor an M2, low-oxidative-stress phenotype after injury.

    Evidence Proteomic profiling, knockdown with functional rescue, ubiquitination assays, spinal cord injury model

    PMID:38896802

    Open questions at the time
    • Specificity factor directing S100A9 recognition not defined
    • Single lab
  11. 2025 High

    Identified the SPRYD3-MYCBP2 complex as a distinct ligase assembly performing non-canonical cysteine ubiquitination of USP11 at Cys318 to control spindle formation and mitotic slippage.

    Evidence Co-IP, ubiquitination assays, USP11 C318 mutagenesis, spindle and cell fate assays

    PMID:41052634

    Open questions at the time
    • How SPRYD3 versus FBXO45 specificity is selected unknown
    • Functional consequence of USP11 cysteine modification on its DUB activity not fully defined
  12. 2025 High

    Defined HNF4α as a degradation substrate, with MYCBP2 building K33/K48-linked chains at specific lysines to modulate lipid metabolism gene expression in liver cancer.

    Evidence In vitro ubiquitination, site-directed mutagenesis of HNF4α K300/K307, proteasome inhibition, Co-IP, in vivo xenograft

    PMID:40181155

    Open questions at the time
    • Specificity factor recruiting HNF4α not identified
    • Role of K33 versus K48 chains mechanistically separated only partially
  13. 2025 Medium

    Added KIF14 as a MYCBP2 degradation target in leukemia, coupling MYCBP2 activity to cell cycle progression and apoptosis.

    Evidence siRNA knockdown, Co-IP, ubiquitination assay, flow cytometry, xenograft

    PMID:42036047

    Open questions at the time
    • Specificity factor and direct binding interface unmapped
    • Single lab
  14. 2025 Medium

    Proposed that TRIB2 scaffolds UCP1 to recruit MYCBP2, linking the ligase to post-translational control of thermogenesis.

    Evidence Co-IP, ubiquitination assay, Trib2 knockout mouse, thermogenesis assays (preprint)

    Open questions at the time
    • Preprint; not peer-reviewed
    • Direct MYCBP2-UCP1 ubiquitination not separated from scaffold effect

Open questions

Synthesis pass · forward-looking unresolved questions
  • How MYCBP2 selects between substrate-specificity factors (FBXO45, SPRYD3, TRIB2 scaffolds) and switches between degradative ubiquitination, target stabilization, and Ran GEF activity in different cell types remains unresolved.
  • No unifying model for context-dependent partner selection
  • Structural basis of non-canonical cysteine ubiquitination undefined
  • Regulatory inputs (phosphorylation, SUMO) integration unmapped

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016874 ligase activity 4 GO:0140096 catalytic activity, acting on a protein 3 GO:0098772 molecular function regulator activity 2
Localization
GO:0005634 nucleus 1 GO:0005829 cytosol 1
Pathway
R-HSA-1266738 Developmental Biology 3 R-HSA-1640170 Cell Cycle 3 R-HSA-392499 Metabolism of proteins 3
Complex memberships
MYCBP2-FBXO45 E3 ligase complexMYCBP2-SPRYD3 E3 ligase complex

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2010 MYCBP2 (E3 ubiquitin ligase) regulates internalization of TRPV1 in peripheral sensory neurons through inhibition of p38 MAPK signaling; loss of MYCBP2 constitutively activates p38 MAPK, which in turn inhibits TRPV1 internalization and prevents desensitization of capsaicin-induced calcium increases, prolonging thermal hyperalgesia. Conditional knockout mouse model (MYCBP2 deficiency in peripheral sensory neurons), p38 MAPK inhibition rescue experiments, calcium imaging, behavioral assays The Journal of biological chemistry High 21098484
2010 Crystal structures of both PHR domains (MmPHR1 and MmPHR2) of mouse Mycbp2/Phr1 were determined, revealing a novel beta-sandwich fold composed of 11 antiparallel beta-strands. MmPHR1 has conserved loops on its apical surface; the structure explains the loss-of-function mutation Gly1092→Glu in the C. elegans ortholog RPM-1. X-ray crystallography (structural determination of PHR domains from Mus musculus Mycbp2) Journal of molecular biology High 20156452
2013 Mycbp2 genetically interacts with Robo2 to regulate axon guidance in the mouse olfactory system; double heterozygous (Mycbp2+/−; Robo2+/−) mice show severe olfactory projection defects, and loss of Mycbp2 causes aberrant expression of Robo2 in dorsal olfactory sensory neurons. Genetic epistasis (double heterozygous mouse mutants), immunohistochemistry, analysis of olfactory sensory neuron projection topography Brain structure & function Medium 23525682
2015 MYCBP2 functions as a guanosine exchange factor (GEF) for the small GTPase Ran in DRG neurons via its RCC1-like domain, facilitating GDP/GTP exchange of Ran in the nucleus. SUMOylated RanGAP1 physically interacts with MYCBP2 and inhibits its E3 ubiquitin ligase activity. Loss of MYCBP2 causes increased nuclear localization of Ran. Co-immunoprecipitation (SUMOylated RanGAP1–MYCBP2 interaction), subcellular fractionation and immunofluorescence (nuclear Ran localization in MYCBP2-deficient DRGs), GDP/GTP exchange assay The Journal of biological chemistry Medium 26304119
2019 MYCBP2 forms an E3 ubiquitin ligase complex with FBXO45; this complex ubiquitylates and promotes proteasomal degradation of the tumor suppressor FBXW7 during prolonged mitotic arrest, thereby promoting mitotic slippage and preventing mitotic cell death. FBXO45 binds to a conserved acidic N-terminal motif of FBXW7 specifically during extended mitotic delay. Co-immunoprecipitation, ubiquitylation assays, proteasome inhibitor rescue, cell fate assays (mitotic slippage vs. cell death), MYCBP2 and FBXO45 knockdown/overexpression Cell death and differentiation High 31285543
2024 MYCBP2 forms a complex with EPHB2 receptor tyrosine kinase facilitated by FBXO45; this complex does not require EPHB2 tyrosine kinase activity and is destabilized by ephrin-B ligand binding. Paradoxically, loss of MYCBP2 increases ubiquitination and decreases protein levels of EPHB2, indicating MYCBP2 stabilizes EPHB2. MYCBP2 is required for efficient EPHB2 signaling responses in cell lines and primary neurons. In C. elegans, the ephrin receptor VAB-1 shows genetic interactions with known MYCBP2 binding proteins. Proteomics screen, biochemical Co-IP, ubiquitination assays, MYCBP2 knockdown in cell lines and primary neurons, C. elegans genetic epistasis eLife High 38289221
2023 MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor signaling; the MYCBP2-EPHB2 complex is facilitated by FBXO45, is independent of EPHB2 kinase activity, and is destabilized by ephrin-B ligands. Loss of MYCBP2 paradoxically increases EPHB2 ubiquitination and reduces its protein levels. Proteomics screen, Co-IP, ubiquitination assays, MYCBP2 knockdown, C. elegans genetics bioRxivpreprint Medium 37693478
2022 RGS12 associates with MYCBP2 and activates it (enhances phosphorylation of MYCBP2) to promote ubiquitination and degradation of KIF2A in synovial fibroblasts, thereby promoting cilia elongation and number; this pathway drives inflammatory arthritis pathogenesis. LC-MS/MS, co-immunoprecipitation, overexpression/knockdown experiments, cilia imaging, in vivo RGS12-deficient mouse model Molecular therapy. Nucleic acids Medium 36700049
2022 RGS12 associates with MYCBP2 in endothelial cells and enhances MYCBP2 phosphorylation to promote ciliogenesis and cilia elongation, driving angiogenesis in inflammatory arthritis. LC/MS and co-IP (RGS12-MYCBP2 interaction), overexpression/knockout experiments, cilia imaging Cell insight Medium 37193553
2023 RGS12 associates with and activates MYCBP2 to ubiquitinate and degrade the cilia protein KIF2A in tumor-associated macrophages, thereby promoting M1 macrophage polarization and antitumor activity in oral squamous cell carcinoma. Co-IP, ubiquitination assays, RGS12 knockout macrophage model, MYCBP2 knockdown, in vitro and in vivo tumor models International journal of oral science Medium 36797232
2024 MYCBP2 promotes ubiquitination and proteasomal degradation of S100A9 in microglia, promoting M2 phenotype polarization and reducing oxidative stress; MYCBP2 knockdown counteracts these beneficial effects in vitro and in vivo. Proteomic profiling (MYCBP2 enrichment in extracellular vesicles), MYCBP2 knockdown with functional rescue assays, ubiquitination assays, in vivo spinal cord injury model Advanced science Medium 38896802
2025 MYCBP2 promotes ubiquitination and degradation of HNF4α via K33- and K48-linked polyubiquitin chains at lysines 300 and 307 of HNF4α, thereby modulating lipid metabolism gene expression in MASH-related hepatocellular carcinoma. In vitro ubiquitination assay, site-directed mutagenesis of HNF4α lysines, proteasome inhibitor treatment, co-IP, MYCBP2 knockdown/overexpression in cell lines and in vivo xenograft Oncogene High 40181155
2025 MYCBP2 forms a novel E3 ligase complex with substrate specificity factor SPRYD3 (distinct from the FBXO45-MYCBP2 complex); SPRYD3-MYCBP2 promotes non-canonical ubiquitination on the deubiquitinase USP11 at cysteine 318, facilitating bipolar spindle formation and mitotic slippage during microtubule-targeting drug treatment. Co-IP (SPRYD3-MYCBP2 complex identification), ubiquitination assays, mutagenesis (USP11 C318), spindle assembly assays, cell fate assays The Journal of biological chemistry High 41052634
2025 TRIB2 acts as a scaffold that binds UCP1 through its pseudokinase domain and recruits MYCBP2 as the E3 ligase to promote UCP1 ubiquitination and proteasomal degradation, linking thermogenic adaptation to post-translational UCP1 regulation. Co-IP (TRIB2-UCP1-MYCBP2 complex), ubiquitination assay, Trib2 knockout mouse model, functional thermogenesis assays bioRxivpreprint Medium
2025 MYCBP2 targets KIF14 for ubiquitin-mediated proteasomal degradation in AML cells; MYCBP2 knockdown increases KIF14 protein stability and partially reverses cell cycle arrest and apoptosis effects caused by MYCBP2 depletion. siRNA knockdown, co-IP, ubiquitination assay, flow cytometry (cell cycle), in vivo xenograft The Journal of biological chemistry Medium 42036047
2023 Loss-of-function variants in MYCBP2 cause a neurodevelopmental disorder (MDCD) with corpus callosum defects, developmental delay, and epilepsy. CRISPR-introduced disease-associated variants in C. elegans rpm-1 produce axonal abnormalities, altered habituation behavior, and abnormal autophagy marker (LGG-1/LC3) accumulation in variants affecting ubiquitin ligase activity, establishing loss of MYCBP2 ubiquitin ligase function as the pathogenic mechanism. CRISPR/Cas9 gene editing in C. elegans, in vivo axon imaging, behavioral assays, autophagy marker analysis, human patient variant identification by exome sequencing Brain : a journal of neurology High 36200388
2002 Ikaros (IKZF1) binds regulatory regions of MYCBP2 and transcriptionally activates its expression in ALL cells; CK2 inhibition (which activates Ikaros) increases MYCBP2 expression in an IKZF1-dependent manner, placing MYCBP2 downstream of the Ikaros/CK2 axis. ChIP (Ikaros binding to MYCBP2 regulatory regions), CK2 inhibitor treatment, IKZF1 deletion correlation analysis, qRT-PCR and Western blot Oncotarget Medium 26517351
2024 In a C. elegans model, introduction of the homologous HSAM-associated MYCBP2 missense variant results in reduced forgetting and increased membrane-bound glutamate receptor levels in relevant neurons, suggesting MYCBP2 normally promotes glutamate receptor removal/degradation to regulate memory. CRISPR knock-in of homologous variant in C. elegans, behavioral forgetting assays, glutamate receptor imaging bioRxivpreprint Low

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2. The Prostate 49 25731699
2015 Clinical significance of high c-MYC and low MYCBP2 expression and their association with Ikaros dysfunction in adult acute lymphoblastic leukemia. Oncotarget 46 26517351
2010 The ubiquitin ligase MYCBP2 regulates transient receptor potential vanilloid receptor 1 (TRPV1) internalization through inhibition of p38 MAPK signaling. The Journal of biological chemistry 45 21098484
2019 FBXO45-MYCBP2 regulates mitotic cell fate by targeting FBXW7 for degradation. Cell death and differentiation 42 31285543
2024 Ginsenoside Rg1 Regulates Immune Microenvironment and Neurological Recovery After Spinal Cord Injury Through MYCBP2 Delivery via Neuronal Cell-Derived Extracellular Vesicles. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 30 38896802
2023 Loss-of-function variants in MYCBP2 cause neurobehavioural phenotypes and corpus callosum defects. Brain : a journal of neurology 28 36200388
2016 miR-92a-3p and MYCBP2 are involved in MS-275-induced and c-myc-mediated TRAIL-sensitivity in melanoma cells. International immunopharmacology 23 27620505
2023 RGS12 represses oral squamous cell carcinoma by driving M1 polarization of tumor-associated macrophages via controlling ciliary MYCBP2/KIF2A signaling. International journal of oral science 19 36797232
2018 Epigenetically regulated miR-1247 functions as a novel tumour suppressor via MYCBP2 in methylator colon cancers. British journal of cancer 19 30318507
2015 High myopia-excavated optic disc anomaly associated with a frameshift mutation in the MYC-binding protein 2 gene (MYCBP2). American journal of ophthalmology 11 25634536
2013 The E3 ubiquitin ligase Mycbp2 genetically interacts with Robo2 to modulate axon guidance in the mouse olfactory system. Brain structure & function 10 23525682
2011 Regulation of neuronal functions by the E3-ubiquitinligase protein associated with MYC (MYCBP2). Communicative & integrative biology 8 22046451
2024 Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function. eLife 7 38289221
2022 Endothelial RGS12 governs angiogenesis in inflammatory arthritis by controlling cilia formation and elongation via MYCBP2 signaling. Cell insight 6 37193553
2015 MYCBP2 Is a Guanosine Exchange Factor for Ran Protein and Determines Its Localization in Neurons of Dorsal Root Ganglia. The Journal of biological chemistry 6 26304119
2022 Regulator of G protein signaling 12 drives inflammatory arthritis by activating synovial fibroblasts through MYCBP2/KIF2A signaling. Molecular therapy. Nucleic acids 5 36700049
2025 MYCBP2-mediated HNF4α ubiquitination reprogrammed lipid metabolism in MASH-associated hepatocellular carcinoma. Oncogene 4 40181155
2023 Dysfunction of ubiquitin protein ligase MYCBP2 leads to cell resilience in human breast cancers. NAR cancer 2 37435531
2010 Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1. Journal of molecular biology 2 20156452
2023 Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function. bioRxiv : the preprint server for biology 1 37693478
2026 Ubiquitin E3 ligase MYCBP2 targets KIF14 and contributes to acute myeloid leukemia progression. The Journal of biological chemistry 0 42036047
2025 The E3 ubiquitin ligase SPRYD3-MYCBP2(PAM) regulates mitotic cell fate and ubiquitination of USP11 to control spindle assembly. The Journal of biological chemistry 0 41052634
2025 First Report of a Familiar MYCBP2 Pathogenic Variant: Expanding the Knowledge of Neurodevelopmental Disorders. Balkan journal of medical genetics : BJMG 0 41200582
2023 Corrigendum to "Endothelial RGS12 governs angiogenesis in inflammatory arthritis by controlling cilia formation and elongation via MYCBP2 signaling" [Cell Insight 1 (2022) 100055]. Cell insight 0 37965246

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