Affinage

SPSB3

SPRY domain-containing SOCS box protein 3 · UniProt Q6PJ21

Length
355 aa
Mass
39.4 kDa
Annotated
2026-06-10
21 papers in source corpus 8 papers cited in narrative 7 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SPSB3 is the substrate-recognition subunit of a CRL5/ECS cullin-RING E3 ubiquitin ligase complex, assembling with ElonginC/B and Cullin5 to direct selected substrates for polyubiquitination and proteasomal degradation (PMID:38418882, PMID:40225996). Its SPRY domain reads short degron motifs on substrates, most rigorously defined for nuclear cGAS, where a conserved C-terminal Asn-Asn (NN) motif is required for SPSB3 recruitment and cGAS turnover; loss of this degradation primes cells for type I interferon signalling, placing SPSB3 as a brake on innate immune activation (PMID:38418882). Beyond cGAS, SPSB3 promotes GSK-3β-phosphorylation-dependent ubiquitination and degradation of the EMT transcription factor SNAIL, restraining tumor metastasis (PMID:29059170), and ubiquitinates the mitochondrial elongation factor TUFM at K259 to modulate cardiomyocyte apoptosis in ischemia/reperfusion injury (PMID:42082827). Substrate selectivity distinguishes SPSB3 from its paralogs: it binds MET and FOG-2 but does not degrade FOG-2, and does not engage RevErbα or Par-4, indicating its SPRY-domain loops recognize substrates through a mechanism distinct from SPSB1/2/4 (PMID:16369487, PMID:15713673, PMID:31607207, PMID:41418348). SPSB3 is dispensable for spermatogenesis and male fertility in mice (PMID:40225996).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2005 Medium

    Established early that SPSB3 shares some binding partners with its paralogs yet has divergent substrate selectivity, framing the SPRY domain as the determinant of specificity.

    Evidence Co-IP of MET across all SSB family members plus NMR structure and mutagenesis defining Par-4 binding residues, showing SSB-3 binds MET but not Par-4

    PMID:15713673 PMID:16369487

    Open questions at the time
    • No E3 ligase activity or substrate degradation demonstrated at this stage
    • Functional consequence of MET binding not established
  2. 2017 Medium

    Identified the first degradation substrate, linking SPSB3 to phospho-dependent control of an EMT driver and to metastasis suppression.

    Evidence Genome-wide siRNA luciferase screen, Co-IP, ubiquitination assays, and in vitro/in vivo metastasis assays showing GSK-3β-dependent SNAIL degradation

    PMID:29059170

    Open questions at the time
    • Degron motif on SNAIL recognized by SPSB3 not defined
    • Direct vs indirect ubiquitination not structurally resolved
  3. 2019 Low

    Refined paralog division of labor by showing SPSB3 does not participate in RevErbα turnover or circadian regulation, unlike SPSB1/4.

    Evidence Cell-based ubiquitin ligase screen, Co-IP, ubiquitination assays, and circadian period measurements (negative result for SPSB3)

    PMID:31607207

    Open questions at the time
    • Negative result reported only within a paralog comparison from a single lab
    • Does not address what distinguishes SPSB3 substrate loops mechanistically
  4. 2024 High

    Defined the molecular basis of substrate recognition: SPSB3 is the CRL5 receptor for nuclear cGAS via an NN minimal degron, establishing SPSB3 as a regulator of innate immune activation.

    Evidence Cryo-EM of nucleosome-bound cGAS–SPSB3, Co-IP, ubiquitylation assays, CRISPR loss-of-function, and type I interferon readouts

    PMID:38418882

    Open questions at the time
    • Whether the NN degron generalizes to other SPSB3 substrates not established
    • Regulation of SPSB3 activity/expression in immune contexts unresolved
  5. 2025 Medium

    Confirmed the canonical ECS architecture (ElonginC/B–Cullin5 recruitment) and tested physiological essentiality, showing SPSB3 is dispensable for male fertility.

    Evidence CRISPR/Cas9 knockout mice with CASA sperm analysis, histology, immunostaining, and TUNEL; Co-IP for ElonginC/B/Cullin5 assembly

    PMID:40225996

    Open questions at the time
    • Phenotypes in other tissues/contexts not examined
    • Possible functional redundancy with paralogs masking a phenotype not tested
  6. 2025 Low

    Demonstrated that binding does not equal degradation: SPSB3 engages FOG-2 through a non-canonical motif but fails to drive its turnover, reinforcing a distinct recognition mechanism.

    Evidence Co-IP, western blot, ubiquitination assays, and motif mutagenesis in a 3T3-L1 adipocyte differentiation model

    PMID:41418348

    Open questions at the time
    • Single lab, Co-IP and western blot only; degradation activity is a negative result
    • Why binding fails to license ubiquitination not mechanistically explained
  7. 2026 Medium

    Extended the substrate repertoire to a mitochondrial target, mapping a specific ubiquitination site and connecting SPSB3 activity to cardiomyocyte survival.

    Evidence CRISPR screen, mass spectrometry/ubiquitin proteomics, Co-IP, K259 site mutagenesis, MG132/CHX, and mouse/cardiomyocyte I/R injury models

    PMID:42082827

    Open questions at the time
    • Degron motif on TUFM recognized by SPSB3 not defined
    • Mixed K48/K63 linkage roles not fully separated

Open questions

Synthesis pass · forward-looking unresolved questions
  • A unifying degron code for SPSB3 across its diverse substrates and the basis for binding-without-degradation outcomes remain unresolved.
  • No general SPRY-domain recognition rule reconciling cGAS, SNAIL, TUFM, FOG-2, and MET
  • Regulation of SPSB3 expression/activity across tissues unknown
  • Determinants converting substrate binding into productive ubiquitination undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 3 GO:0016874 ligase activity 2 GO:0060090 molecular adaptor activity 2
Localization
GO:0005634 nucleus 1
Pathway
R-HSA-392499 Metabolism of proteins 3 R-HSA-168256 Immune System 1
Partners
CGASCUL5ELOBELOCFOG-2METSNAILTUFM
Complex memberships
CRL5/ECS (ElonginB/C–Cullin5) E3 ubiquitin ligase

Evidence

Reading pass · 7 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2024 SPSB3 acts as the substrate receptor for the CRL5 (cullin-RING ubiquitin ligase 5) complex and directly targets nuclear cGAS for ubiquitylation and proteasomal degradation. A cryo-EM structure of nucleosome-bound cGAS complexed with SPSB3 revealed that a conserved Asn-Asn (NN) minimal degron motif at the C-terminus of cGAS is required for SPSB3 recruitment, ubiquitylation, and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling. Cryo-EM structure determination, Co-immunoprecipitation, ubiquitylation assays, CRISPR/loss-of-function experiments, type I interferon signalling readouts Nature High 38418882
2017 SPSB3 functions as an E3 ligase component that promotes polyubiquitination and proteasomal degradation of the EMT transcription factor SNAIL in a manner dependent on prior GSK-3β phosphorylation of SNAIL. SPSB3 overexpression inhibits tumor metastasis in vitro and in vivo by reducing SNAIL levels. Genome-wide siRNA screen (luciferase-based), co-immunoprecipitation, ubiquitination assays, overexpression/knockdown with in vitro and in vivo metastasis assays Oncogene Medium 29059170
2005 SSB-3 (SPSB3) binds MET (hepatocyte growth factor receptor) similarly to the other SSB family members. Negative finding specific to SPSB3: unlike SSB-1, SSB-2, and SSB-4, SSB-3 does not bind Par-4 (prostate apoptosis response protein-4), indicating its SPRY domain loop regions differ functionally from the other paralogs. Co-immunoprecipitation (binding to MET); NMR structure of SSB-2 SPRY domain with mutational analysis defining Par-4 binding residues; direct binding assays for Par-4 across SSB family members Nature structural & molecular biology / The Journal of biological chemistry Medium 15713673 16369487
2019 SPSB1 and SPSB4, but not SPSB2 and SPSB3, interact with and facilitate ubiquitination and degradation of the circadian clock protein RevErbα, and regulate circadian period. SPSB3 does not participate in this substrate pathway. Cell-based functional ubiquitin ligase screen, co-immunoprecipitation, ubiquitination assays, circadian period measurements Journal of biological rhythms Low 31607207
2025 SPSB3 binds FOG-2 independently of the D-L-N-N-N motif recognized by SPSB1/2/4, but SPSB3 fails to trigger FOG-2 ubiquitin-proteasome-dependent degradation, demonstrating that SPSB3 employs a substrate-recognition mechanism distinct from SPSB1/2/4 and is not sufficient for FOG-2 degradation. Co-immunoprecipitation, western blot, ubiquitination assays, motif mutagenesis, 3T3-L1 adipocyte differentiation model Biochemical and biophysical research communications Low 41418348
2026 SPSB3 binds the mitochondrial protein TUFM (Tu translation elongation factor, mitochondrial) and promotes its K48- and K63-linked ubiquitination at the K259 residue, leading to TUFM degradation. SPSB3 inhibition prevents TUFM ubiquitination and degradation, attenuating cardiomyocyte apoptosis in myocardial ischemia/reperfusion injury models. CRISPR/Cas9 high-throughput screening, mass spectrometry, ubiquitin-modified proteomics, co-immunoprecipitation, western blot, amino acid site mutagenesis (K259), MG132/cycloheximide treatment, mouse and cardiomyocyte I/R injury models Cell biology and toxicology Medium 42082827
2025 SPSB3 interacts with ElonginC/B and recruits Cullin5 to form the ECS E3 ligase complex. Knockout of Spsb3 in mice (via CRISPR/Cas9) does not produce defects in sperm quality, fertility, or testis histology, demonstrating that SPSB3 is not essential for spermatogenesis or male fertility under physiological conditions. CRISPR/Cas9 knockout mice, CASA sperm analysis, histology, immunostaining, TUNEL assay American journal of translational research Medium 40225996

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2000 Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease. Biological chemistry 105 10782989
2005 The SPRY domain of SSB-2 adopts a novel fold that presents conserved Par-4-binding residues. Nature structural & molecular biology 64 16369487
2016 Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications. Frontiers in microbiology 59 27881980
2024 The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Nature 51 38418882
2005 The SPRY domain-containing SOCS box protein 1 (SSB-1) interacts with MET and enhances the hepatocyte growth factor-induced Erk-Elk-1-serum response element pathway. The Journal of biological chemistry 46 15713673
2017 SPSB3 targets SNAIL for degradation in GSK-3β phosphorylation-dependent manner and regulates metastasis. Oncogene 43 29059170
2017 Colorectal cancer stages transcriptome analysis. PloS one 31 29182684
2012 Genomic signatures for predicting survival and adjuvant chemotherapy benefit in patients with non-small-cell lung cancer. BMC medical genomics 31 22748043
1990 Signal strains that can detect certain DNA replication and membrane mutants of Escherichia coli: isolation of a new ssb allele, ssb-3. Journal of bacteriology 21 2142938
2019 Complexed crystal structure of SSB reveals a novel single-stranded DNA binding mode (SSB)3:1: Phe60 is not crucial for defining binding paths. Biochemical and biophysical research communications 16 31604524
2005 Repeat-length-independent broad-spectrum shuffling, a novel method of generating a random chimera library in vivo. Applied and environmental microbiology 15 15691927
1992 Interaction of the heat shock protein GroEL of Escherichia coli with single-stranded DNA-binding protein: suppression of ssb-113 by groEL46. Journal of bacteriology 10 1374377
2019 The E3 Ligases Spsb1 and Spsb4 Regulate RevErbα Degradation and Circadian Period. Journal of biological rhythms 8 31607207
2019 A SPRY domain-containing SOCS box protein 3 (SPSB3) involved in the regulation of cytokine production in granulocytes of Crassostrea gigas. Developmental and comparative immunology 6 30711451
1999 A DNA probe specific to Streptococcus sobrinus. Oral microbiology and immunology 6 10551167
2021 Genomic analysis of host gene responses to cerebral Plasmodium falciparum malaria. Immunity, inflammation and disease 5 33942992
2018 Combination of anti-early apoptotic cell autoantibodies and anti-SSA autoantibodies in lupus nephritis. Cellular and molecular biology (Noisy-le-Grand, France) 3 30403595
2024 Keeping cGAS in check: SPSB3 promotes nuclear cGAS degradation for maintaining immune homeostasis. Molecular cell 1 38701740
2026 SPSB3-mediated K48- and K63- linked ubiquitination and degradation of TUFM promote apoptosis induced by myocardial ischemia/reperfusion injury. Cell biology and toxicology 0 42082827
2025 Spsb3 is not essential for spermatogenesis and male fertility in mice. American journal of translational research 0 40225996
2025 SPSB proteins regulate adipocyte differentiation by targeting FOG-2 for proteasomal degradation. Biochemical and biophysical research communications 0 41418348

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