{"gene":"SUMO3","run_date":"2026-04-28T21:42:57","timeline":{"discoveries":[{"year":2001,"finding":"SUMO-2 and SUMO-3 contain an internal consensus SUMO modification site (ψKXE), allowing SAE1/SAE2 (E1) and Ubc9 (E2) to catalyze formation of polymeric SUMO-2 and SUMO-3 chains on protein substrates in vitro; SUMO-2 chains were also detected in vivo. This chain-forming capacity is not shared by SUMO-1.","method":"In vitro conjugation assay with purified recombinant components; in vivo detection of SUMO-2 chains; sequence analysis of ψKXE motif","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with purified components plus in vivo validation; foundational highly-cited paper (694 citations)","pmids":["11451954"],"is_preprint":false},{"year":2005,"finding":"Solution NMR structure of SUMO-3 C47S (residues 14–92) revealed a β-β-α-β-β-α-β ubiquitin fold; chemical shift perturbation mapping identified the Ubc9-binding surface on SUMO-3 as residing primarily on the hydrophilic side of the β-sheet, with negatively charged and hydrophobic residues that are electrostatically complementary to the positively charged Ubc9 surface.","method":"NMR solution structure determination; chemical shift perturbation assay for Ubc9 binding surface mapping","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 — NMR structure with functional binding surface validation","pmids":["15723523"],"is_preprint":false},{"year":2003,"finding":"SUMO-3 (and SUMO-1) modifies C/EBPα at Lys159 within the synergy control (SC) motif; PIASy acts as an E3 ligase enhancing both SUMO-1 and SUMO-3 modification of C/EBPα in vivo and in vitro. SUMO modification at the SC motif limits transcriptional synergy at compound response elements, as a K159R mutation abolished SUMO modification and enhanced synergistic transactivation.","method":"In vitro SUMOylation with purified recombinant components; in vivo SUMOylation assays; site-directed mutagenesis (K159R); transcriptional reporter assays; Co-IP with Ubc9","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution plus mutagenesis plus functional transcription assay; replicated across multiple orthogonal methods","pmids":["12511558"],"is_preprint":false},{"year":2003,"finding":"C/EBPβ-1 (but not C/EBPβ-2) is conjugated by SUMO-2 and SUMO-3 at Lys173, dependent on its extreme N-terminus; mutation of Lys173 relieves C/EBPβ-1-mediated repression of the cyclin D1 promoter without altering subnuclear localization, indicating SUMO-2/3 modification mediates transcriptional repression by C/EBPβ-1.","method":"In vivo SUMOylation assay; site-directed mutagenesis (K173R); transcriptional reporter assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — clean mutagenesis with functional readout, single lab","pmids":["12810706"],"is_preprint":false},{"year":2005,"finding":"SUMO-3 conjugation to PML stabilizes its nuclear localization: PML is covalently modified by SUMO-3 (shown by co-IP), SUMO-3 depletion by siRNA markedly reduces PML nuclear body number and integrity (rescued by exogenous SUMO-3 but not SUMO-1 or SUMO-2), and SUMO-3 oligomerization is required for PML nuclear retention. SUMO-2 and SUMO-3 (but not SUMO-1) also localize to nucleoli.","method":"Co-immunoprecipitation; siRNA knockdown; rescue with SUMO conjugation-defective mutant; immunofluorescence localization","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP plus siRNA rescue experiment with specific functional readout, single lab","pmids":["15940266"],"is_preprint":false},{"year":2005,"finding":"SUMO-3 enhances androgen receptor (AR) transcriptional activity in LNCaP prostate cancer cells through a mechanism independent of AR sumoylation sites and independent of SUMO-3's own conjugation function, as shown by mutational analysis of both AR sumoylation sites and SUMO-3; stable SUMO-3 overexpression enhances androgen-dependent LNCaP proliferation.","method":"Yeast functional screen; mutational analysis of AR sumoylation sites and SUMO-3 conjugation function; transcriptional reporter assay; stable overexpression; siRNA knockdown; proliferation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis plus functional reporter assay plus siRNA, single lab","pmids":["16361251"],"is_preprint":false},{"year":2014,"finding":"SUMO3 (and SUMO1) modify ALS-linked SOD1 mutant proteins at Lys75 in a motoneuronal cell line; SUMO3 modification (but not SUMO1) significantly increases the stability of mutant SOD1 proteins and accelerates their intracellular aggregate formation.","method":"In vivo SUMOylation assay in motoneuronal cell line; site-directed mutagenesis of SOD1 Lys75 and Lys9; stability and aggregate formation assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis identifying specific sites plus functional aggregation assay, single lab","pmids":["24971881"],"is_preprint":false},{"year":2014,"finding":"SUMO2 is essential for mouse embryonic development (Sumo2−/− embryos die ~E10.5 with severe developmental delay), while SUMO3 is dispensable (Sumo3−/− mice are viable); however, combined reduction of SUMO2 and SUMO3 (Sumo2+/−;Sumo3−/−) causes near-lethal growth defects, indicating functional redundancy and that dosage rather than isoform-specific function is critical.","method":"Genetic knockout mouse models; timed embryonic lethality analysis; compound heterozygote/null crosses","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 — clean in vivo genetic epistasis with defined developmental phenotype, replicated across multiple genotypes","pmids":["24891386"],"is_preprint":false},{"year":2011,"finding":"Using SILAC-based quantitative proteomics after HA-SUMO3 immunoprecipitation, 188 putative SUMO3-conjugated proteins were identified in neuroblastoma cells exposed to oxygen/glucose deprivation (OGD), including transcription factors, coregulators, and PIAS2/PIAS4 ligases. Furthermore, SUMO2/3 gene silencing completely blocked OGD-induced protein ubiquitination, demonstrating crosstalk between SUMO3 conjugation and the ubiquitin pathway.","method":"SILAC quantitative proteomics; HA-SUMO3 immunoprecipitation; LC-MS/MS; siRNA gene silencing with ubiquitination readout","journal":"Journal of proteome research","confidence":"Medium","confidence_rationale":"Tier 2 — MS-based interactome plus genetic silencing with defined functional crosstalk readout, single lab","pmids":["22082260"],"is_preprint":false},{"year":2018,"finding":"SUMO1 and SUMO3 exert differential effects on PKR: SUMO3 expression causes PKR to concentrate around the perinuclear membrane and relocalize to nuclear dots, reduces PKR and eIF-2α activation upon viral infection or dsRNA transfection, and promotes caspase-dependent EMCV-induced PKR degradation. In contrast, SUMO1 activates PKR and eIF-2α even without viral infection.","method":"Overexpression of SUMO1 vs SUMO3; immunofluorescence localization; Western blot for PKR/eIF-2α phosphorylation; viral infection assays; caspase inhibitor experiments","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — direct comparison of isoforms with multiple functional readouts (localization, activation, stability), single lab","pmids":["29352251"],"is_preprint":false},{"year":2018,"finding":"SUMO2 and SUMO3 (but not SUMO1) redundantly prevent a noncanonical type I interferon response; loss of sumoylation triggers spontaneous IFN production independent of IRF3, IRF7, and all known IFN-inducing pathways.","method":"Genetic loss-of-function (SUMO2 and SUMO3 knockout/knockdown); IFN production assays; epistasis with IRF3/IRF7 knockouts","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — clean genetic epistasis with defined pathway placement and specific phenotypic readout","pmids":["29891701"],"is_preprint":false},{"year":2019,"finding":"SUMO3 (but not SUMO1 or SUMO2) forms polymeric chains conjugated to MAVS upon poly(dA:dT) stimulation in human keratinocytes; SUMO3 chain conjugation to MAVS enhances MAVS aggregation, which drives IFN-β secretion downstream of RIG-I. Inhibition of SUMOylation (by ginkgolic acid or Ubc9 siRNA) blocked IFN-β secretion.","method":"Co-immunoprecipitation for SUMO3-MAVS conjugation; SUMO chain detection assay; Ubc9 siRNA; ginkgolic acid inhibition; IFN-β ELISA; MAVS aggregation assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus functional inhibition with defined pathway outcome, single lab","pmids":["31806367"],"is_preprint":false},{"year":2019,"finding":"PIAS1, together with SUMO3, mediates AR cytosolic translocation and subsequent proteasomal degradation via MDM2; AR sumoylation at Lys386 (SUMO-acceptor) and ubiquitination at Lys845 cooperate for AR nuclear export and degradation. Moreover, PIAS1 itself is modified by SUMO3 at Lys117, and this PIAS1 sumoylation is required for AR cytoplasmic redistribution and recruitment of MDM2 to drive AR ubiquitination and degradation.","method":"Immunostaining for AR localization; co-immunoprecipitation; site-directed mutagenesis (AR K386R, K845; PIAS1 K117); Western blot for ubiquitination and degradation; siRNA knockdown","journal":"Cell communication and signaling : CCS","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis plus Co-IP plus localization assay with functional degradation readout, single lab","pmids":["31752909"],"is_preprint":false},{"year":2023,"finding":"SUMO-3 (but not SUMO-1) promotes ubiquitin-dependent proteasomal and lysosomal degradation of TRIM55; TRIM55 contains two SUMO-interacting motifs (SIMs) that mediate this effect, as SIM-mutated TRIM55 shows increased stability, reduced polyubiquitination, and altered subcellular localization.","method":"Overexpression of SUMO-3 vs SUMO-1; SIM mutagenesis; proteasome/lysosome inhibitor assays; polyubiquitination assay; immunofluorescence microscopy","journal":"Biochemistry and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis of SIM motifs plus ubiquitination assay plus localization, single lab","pmids":["37703582"],"is_preprint":false},{"year":2008,"finding":"In SUMO1-null mice, SUMO2 and/or SUMO3 compensate for SUMO1 function by sumoylating SUMO1 target proteins including RanGAP1; RanGAP1 localization is affected but PML nuclear bodies still form, demonstrating functional redundancy between SUMO isoforms in vivo.","method":"Genetic knockout mouse (SUMO1-null); immunofluorescence for RanGAP1 and PML localization; Western blot for sumoylation status","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo genetic model with direct localization readout for SUMO1 targets","pmids":["19033381"],"is_preprint":false},{"year":2011,"finding":"SUMO3 transcription (but not SUMO2) is down-regulated by oxidative stress; Sp1 binds the Sumo3 gene promoter, and oxidative stress causes Sp1 oxidation and suppression of Sp1-DNA binding, thereby selectively reducing SUMO3 expression.","method":"qRT-PCR for SUMO2/SUMO3 mRNA; promoter characterization; chromatin immunoprecipitation (ChIP) for Sp1 binding; Sp1 oxidation assay","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP plus functional promoter analysis with direct mechanistic link, single lab","pmids":["21291420"],"is_preprint":false}],"current_model":"SUMO3 is a ubiquitin-like modifier that, together with SUMO2 but distinct from SUMO1, forms polymeric chains via its internal ψKXE consensus site using the SAE1/SAE2 E1 and Ubc9 E2 enzymes; it covalently modifies specific substrates (including PML, C/EBPα, C/EBPβ-1, SOD1 mutants, AR, PKR, MAVS, and PIAS1) with functional consequences including regulation of nuclear localization, transcriptional synergy, protein stability and degradation, innate immune signaling (IFN-β induction via MAVS aggregation and suppression of a noncanonical IFN pathway), and antiviral responses, while its NMR solution structure reveals a ubiquitin fold with a defined negatively charged Ubc9-binding surface on the β-sheet."},"narrative":{"teleology":[{"year":2001,"claim":"Establishing that SUMO2/3, unlike SUMO1, can form polymeric chains resolved how SUMO paralogs differ mechanistically and identified the ψKXE internal site as the basis for chain elongation via the SAE1/SAE2–Ubc9 cascade.","evidence":"In vitro reconstitution with purified E1/E2 and recombinant SUMO proteins plus in vivo chain detection","pmids":["11451954"],"confidence":"High","gaps":["No E3 ligase involvement characterized for chain formation","Chain topology and length regulation undefined","Functional consequences of chains vs. mono-SUMO3 not separated"]},{"year":2003,"claim":"Demonstrating that SUMO3 modifies transcription factors C/EBPα and C/EBPβ-1 at specific lysines established that SUMO3 conjugation directly regulates transcriptional output—limiting synergistic transactivation (C/EBPα) and mediating transcriptional repression (C/EBPβ-1).","evidence":"In vitro and in vivo SUMOylation assays with site-directed mutagenesis (K159R, K173R) coupled to transcriptional reporter assays","pmids":["12511558","12810706"],"confidence":"High","gaps":["Mechanism by which SUMO3 at the synergy control motif attenuates transcription not defined","Chromatin-level effects not examined"]},{"year":2005,"claim":"The NMR structure of SUMO3 and mapping of its Ubc9-binding surface revealed the electrostatic complementarity underlying E2 recognition, providing a structural basis for conjugation specificity.","evidence":"NMR solution structure determination with chemical shift perturbation mapping of the Ubc9 interface","pmids":["15723523"],"confidence":"High","gaps":["No co-crystal structure of the SUMO3–Ubc9 complex","Structural basis for SUMO2 vs. SUMO3 discrimination by substrates not addressed"]},{"year":2005,"claim":"Showing that SUMO3 is specifically required for PML nuclear body integrity—and that SUMO3 oligomerization is needed for PML nuclear retention—established a non-redundant isoform-specific role distinct from SUMO1 and SUMO2.","evidence":"siRNA depletion of SUMO3 with rescue by wild-type but not conjugation-defective SUMO3; immunofluorescence","pmids":["15940266"],"confidence":"Medium","gaps":["Mechanism by which SUMO3 chains specifically retain PML in nuclear bodies not defined","Whether SUMO3 oligomerization acts via SIM-mediated interactions was not tested"]},{"year":2005,"claim":"SUMO3 enhances androgen receptor transcriptional activity and prostate cancer cell proliferation through a conjugation-independent mechanism, revealing a non-covalent function for SUMO3.","evidence":"Mutational analysis of AR sumoylation sites and SUMO3 conjugation function; reporter assay and proliferation assay in LNCaP cells","pmids":["16361251"],"confidence":"Medium","gaps":["Non-covalent mechanism of action uncharacterized","Direct binding partner mediating conjugation-independent effect unknown"]},{"year":2008,"claim":"In vivo compensation by SUMO2/3 for SUMO1 loss in modifying RanGAP1 demonstrated broad functional redundancy among SUMO paralogs at the organismal level.","evidence":"SUMO1-null mouse with immunofluorescence and Western blot analysis of RanGAP1 and PML sumoylation status","pmids":["19033381"],"confidence":"Medium","gaps":["Which E3 ligases redirect SUMO2/3 to SUMO1 targets not identified","Whether compensatory modification is qualitatively equivalent unclear"]},{"year":2011,"claim":"Proteomic identification of 188 SUMO3 substrates under ischemia and the finding that SUMO2/3 silencing blocks stress-induced ubiquitination established a direct crosstalk between the SUMO3 and ubiquitin pathways under cellular stress.","evidence":"SILAC-based quantitative proteomics with HA-SUMO3 IP in neuroblastoma cells; siRNA-mediated SUMO2/3 depletion with ubiquitination readout","pmids":["22082260"],"confidence":"Medium","gaps":["Individual SUMO3 substrates not validated by orthogonal methods","Molecular link between SUMO3 conjugation and ubiquitin ligase recruitment not identified"]},{"year":2011,"claim":"Selective transcriptional downregulation of SUMO3 (but not SUMO2) by oxidative stress through Sp1 oxidation revealed that SUMO3 abundance is dynamically regulated, providing a mechanism for stress-dependent shifts in the SUMO2/3 ratio.","evidence":"qRT-PCR, promoter analysis, and ChIP for Sp1 binding under oxidative stress","pmids":["21291420"],"confidence":"Medium","gaps":["Whether reduced SUMO3 alters the poly-SUMO chain landscape under stress not tested","Sp1 oxidation site not mapped"]},{"year":2014,"claim":"Genetic analysis in mice established that SUMO3 is individually dispensable for viability but becomes essential in combination with reduced SUMO2, proving dosage-dependent functional redundancy rather than strict isoform-specific roles in development.","evidence":"Sumo2 and Sumo3 single and compound knockout mice; timed embryonic analysis","pmids":["24891386"],"confidence":"High","gaps":["Specific developmental processes requiring SUMO2/3 dosage not identified","Whether tissue-specific expression differences contribute to the dosage requirement unclear"]},{"year":2018,"claim":"SUMO2/3 were shown to actively suppress a noncanonical type I interferon response independent of known IFN-inducing pathways, positioning SUMOylation as a constitutive checkpoint on innate immune activation.","evidence":"SUMO2/3 genetic knockout combined with epistasis analysis using IRF3/IRF7 knockouts; IFN production assays","pmids":["29891701"],"confidence":"High","gaps":["Identity of the SUMO2/3-modified target(s) that suppress noncanonical IFN unknown","Whether this reflects mono- vs. poly-SUMO modification not determined"]},{"year":2019,"claim":"SUMO3 poly-chain conjugation to MAVS was shown to drive MAVS aggregation and IFN-β production in response to cytosolic DNA sensing, establishing a direct mechanistic link between SUMO3 chains and innate antiviral signaling.","evidence":"Co-IP of SUMO3-MAVS; MAVS aggregation assay; Ubc9 siRNA and ginkgolic acid inhibition; IFN-β ELISA in keratinocytes","pmids":["31806367"],"confidence":"Medium","gaps":["SUMO3 conjugation sites on MAVS not mapped","E3 ligase mediating MAVS SUMO3 modification not identified"]},{"year":2019,"claim":"SUMO3 modification of PIAS1 at K117 was shown to be required for AR cytoplasmic redistribution and MDM2-mediated AR ubiquitination and proteasomal degradation, establishing a SUMO3→ubiquitin→degradation cascade for AR.","evidence":"Site-directed mutagenesis of PIAS1 K117 and AR K386/K845; Co-IP; AR localization by immunostaining; degradation assays","pmids":["31752909"],"confidence":"Medium","gaps":["Whether SUMO3 modification of PIAS1 alters its E3 ligase activity broadly or is AR-specific unknown","In vivo relevance in prostate tissue not tested"]},{"year":2023,"claim":"Demonstrating that SUMO3 promotes TRIM55 degradation through SIM-dependent ubiquitination via both proteasomal and lysosomal routes generalized the SUMO3-to-ubiquitin degradation mechanism to a non-covalent (SIM-mediated) mode of action.","evidence":"SUMO3 overexpression; SIM mutagenesis in TRIM55; proteasome and lysosome inhibitor assays; polyubiquitination assay","pmids":["37703582"],"confidence":"Medium","gaps":["Whether SUMO3 acts as a direct bridging factor or recruits a SUMO-targeted ubiquitin ligase (STUbL) for TRIM55 degradation not determined","Physiological context of TRIM55–SUMO3 interaction not established"]},{"year":null,"claim":"Key unresolved questions include: the identity of SUMO3-specific substrates vs. shared SUMO2/3 substrates at endogenous expression levels, the E3 ligases and deconjugases that confer SUMO3 specificity in innate immune signaling, and the structural basis for differential recognition of SUMO3 chains by SIM-containing effectors.","evidence":"","pmids":[],"confidence":"Low","gaps":["No systematic endogenous-level SUMO3-specific substrate catalog exists","SUMO3 chain readers/decoders not comprehensively identified","No structural model of a SUMO3 poly-chain bound to a SIM-containing effector"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[0,2,3,4,6,11,12]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4,9]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[4]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,2,3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2,3,8,12,13]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[10,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[2,3,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[7]}],"complexes":[],"partners":["UBC9","PML","MAVS","PIAS1","PIASY","AR","CEBPA","CEBPB"],"other_free_text":[]},"mechanistic_narrative":"SUMO3 is a ubiquitin-like post-translational modifier that conjugates to target proteins via the SAE1/SAE2 E1 and Ubc9 E2 enzymatic cascade and forms polymeric chains through an internal ψKXE consensus site, a capacity shared with SUMO2 but not SUMO1 [PMID:11451954]. SUMO3 modification regulates diverse nuclear processes including transcriptional synergy control (C/EBPα, C/EBPβ-1), PML nuclear body integrity, androgen receptor stability and degradation via PIAS1/MDM2-mediated ubiquitination, and innate immune signaling through MAVS aggregation-driven IFN-β induction and suppression of a noncanonical type I interferon response [PMID:12511558, PMID:15940266, PMID:31752909, PMID:31806367, PMID:29891701]. Although SUMO3 is largely functionally redundant with SUMO2—Sumo3-null mice are viable whereas Sumo2-null embryos die at ~E10.5—combined dosage reduction reveals essential shared roles in development, and SUMO2/3 can compensate for SUMO1 loss in modifying canonical SUMO1 substrates such as RanGAP1 [PMID:24891386, PMID:19033381]. The NMR solution structure of SUMO3 adopts a ββαββαβ ubiquitin fold, with a negatively charged β-sheet surface that mediates electrostatic recognition of Ubc9 [PMID:15723523]."},"prefetch_data":{"uniprot":{"accession":"P55854","full_name":"Small ubiquitin-related modifier 3","aliases":["SMT3 homolog 1","SUMO-2","Ubiquitin-like protein SMT3A","Smt3A"],"length_aa":103,"mass_kda":11.6,"function":"Ubiquitin-like protein which can be covalently attached to target lysines either as a monomer or as a lysine-linked polymer. Does not seem to be involved in protein degradation and may function as an antagonist of ubiquitin in the degradation process. Plays a role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Covalent attachment to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by an E3 ligase such as PIAS1-4, RANBP2 or CBX4 (PubMed:11451954, PubMed:18538659, PubMed:21965678). Plays a role in the regulation of sumoylation status of SETX (PubMed:24105744)","subcellular_location":"Cytoplasm; Nucleus; Nucleus, PML body","url":"https://www.uniprot.org/uniprotkb/P55854/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SUMO3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SUMO3","total_profiled":1310},"omim":[{"mim_id":"617842","title":"PROTEASOME 26S SUBUNIT, NON-ATPase, 1; PSMD1","url":"https://www.omim.org/entry/617842"},{"mim_id":"617470","title":"UBIQUITIN-SPECIFIC PEPTIDASE-LIKE 1; USPL1","url":"https://www.omim.org/entry/617470"},{"mim_id":"614637","title":"DESUMOYLATING ISOPEPTIDASE 1; DESI1","url":"https://www.omim.org/entry/614637"},{"mim_id":"613644","title":"ACTIVATING TRANSCRIPTION FACTOR 7-INTERACTING PROTEIN; ATF7IP","url":"https://www.omim.org/entry/613644"},{"mim_id":"613295","title":"UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 2; UBA2","url":"https://www.omim.org/entry/613295"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Supported"},{"location":"Calyx","reliability":"Additional"},{"location":"Connecting piece","reliability":"Additional"},{"location":"Flagellar centriole","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SUMO3"},"hgnc":{"alias_symbol":["SMT3A"],"prev_symbol":["SMT3H1"]},"alphafold":{"accession":"P55854","domains":[{"cath_id":"3.10.20.90","chopping":"15-86","consensus_level":"high","plddt":91.0617,"start":15,"end":86}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P55854","model_url":"https://alphafold.ebi.ac.uk/files/AF-P55854-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P55854-F1-predicted_aligned_error_v6.png","plddt_mean":81.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SUMO3","jax_strain_url":"https://www.jax.org/strain/search?query=SUMO3"},"sequence":{"accession":"P55854","fasta_url":"https://rest.uniprot.org/uniprotkb/P55854.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P55854/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P55854"}},"corpus_meta":[{"pmid":"11451954","id":"PMC_11451954","title":"Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11451954","citation_count":694,"is_preprint":false},{"pmid":"24891386","id":"PMC_24891386","title":"SUMO2 is essential while SUMO3 is dispensable for mouse embryonic development.","date":"2014","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/24891386","citation_count":161,"is_preprint":false},{"pmid":"19033381","id":"PMC_19033381","title":"Loss of SUMO1 in mice affects RanGAP1 localization and formation of PML nuclear bodies, but is not lethal as it can be compensated by SUMO2 or SUMO3.","date":"2008","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/19033381","citation_count":126,"is_preprint":false},{"pmid":"12511558","id":"PMC_12511558","title":"A synergy control motif within the attenuator domain of CCAAT/enhancer-binding protein alpha inhibits transcriptional synergy through its PIASy-enhanced modification by SUMO-1 or SUMO-3.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12511558","citation_count":126,"is_preprint":false},{"pmid":"9119407","id":"PMC_9119407","title":"SMT3A, a human homologue of the S. cerevisiae SMT3 gene, maps to chromosome 21qter and defines a novel gene family.","date":"1997","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/9119407","citation_count":102,"is_preprint":false},{"pmid":"15940266","id":"PMC_15940266","title":"Stabilization of PML nuclear localization by conjugation and oligomerization of SUMO-3.","date":"2005","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/15940266","citation_count":90,"is_preprint":false},{"pmid":"12810706","id":"PMC_12810706","title":"Modification of CCAAT/enhancer-binding protein-beta by the small ubiquitin-like modifier (SUMO) family members, SUMO-2 and SUMO-3.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12810706","citation_count":74,"is_preprint":false},{"pmid":"22082260","id":"PMC_22082260","title":"Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics.","date":"2011","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/22082260","citation_count":59,"is_preprint":false},{"pmid":"29891701","id":"PMC_29891701","title":"SUMO2 and SUMO3 redundantly prevent a noncanonical type I interferon response.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/29891701","citation_count":47,"is_preprint":false},{"pmid":"16361251","id":"PMC_16361251","title":"SUMO-3 enhances androgen receptor transcriptional activity through a sumoylation-independent mechanism in prostate cancer cells.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16361251","citation_count":38,"is_preprint":false},{"pmid":"9891849","id":"PMC_9891849","title":"Characterization of mouse ubiquitin-like SMT3A and SMT3B cDNAs and gene/pseudogenes.","date":"1998","source":"Biochemistry and molecular biology international","url":"https://pubmed.ncbi.nlm.nih.gov/9891849","citation_count":37,"is_preprint":false},{"pmid":"15723523","id":"PMC_15723523","title":"Solution structure of human SUMO-3 C47S and its binding surface for Ubc9.","date":"2005","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15723523","citation_count":30,"is_preprint":false},{"pmid":"21291420","id":"PMC_21291420","title":"SUMO2 and SUMO3 transcription is differentially regulated by oxidative stress in an Sp1-dependent manner.","date":"2011","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/21291420","citation_count":28,"is_preprint":false},{"pmid":"24971881","id":"PMC_24971881","title":"SUMO3 modification accelerates the aggregation of ALS-linked SOD1 mutants.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24971881","citation_count":28,"is_preprint":false},{"pmid":"24617894","id":"PMC_24617894","title":"Recombinant production of the antimicrobial peptide NZ17074 in Pichia pastoris using SUMO3 as a fusion partner.","date":"2014","source":"Letters in applied microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/24617894","citation_count":26,"is_preprint":false},{"pmid":"31752909","id":"PMC_31752909","title":"SUMO3 modification by PIAS1 modulates androgen receptor cellular distribution and stability.","date":"2019","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/31752909","citation_count":22,"is_preprint":false},{"pmid":"22595540","id":"PMC_22595540","title":"Correlation of increased hippocampal Sumo3 with spatial learning ability in old C57BL/6 mice.","date":"2012","source":"Neuroscience letters","url":"https://pubmed.ncbi.nlm.nih.gov/22595540","citation_count":19,"is_preprint":false},{"pmid":"29352251","id":"PMC_29352251","title":"Differential effects of SUMO1 and SUMO3 on PKR activation and stability.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29352251","citation_count":17,"is_preprint":false},{"pmid":"31806367","id":"PMC_31806367","title":"Formation of SUMO3-conjugated chains of MAVS induced by poly(dA:dT), a ligand of RIG-I, enhances the aggregation of MAVS that drives the secretion of interferon-β in human keratinocytes.","date":"2019","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/31806367","citation_count":13,"is_preprint":false},{"pmid":"34145454","id":"PMC_34145454","title":"Antagonism between SUMO1/2 and SUMO3 regulates SUMO conjugate levels and fine-tunes immunity.","date":"2021","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/34145454","citation_count":9,"is_preprint":false},{"pmid":"33785433","id":"PMC_33785433","title":"lncRNA-SUMO3 and lncRNA-HDMO13 modulate the inflammatory response by binding miR-21 and miR-142a-3p in grass carp.","date":"2021","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33785433","citation_count":8,"is_preprint":false},{"pmid":"22296450","id":"PMC_22296450","title":"A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL.","date":"2012","source":"British journal of haematology","url":"https://pubmed.ncbi.nlm.nih.gov/22296450","citation_count":8,"is_preprint":false},{"pmid":"30593901","id":"PMC_30593901","title":"Fish SUMO3 functions as a critical antiviral molecule against iridovirus and nodavirus.","date":"2018","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30593901","citation_count":6,"is_preprint":false},{"pmid":"39183358","id":"PMC_39183358","title":"SUMO3 inhibition by butyric acid suppresses cell viability and glycolysis and promotes gemcitabine antitumor activity in pancreatic cancer.","date":"2024","source":"Biology direct","url":"https://pubmed.ncbi.nlm.nih.gov/39183358","citation_count":6,"is_preprint":false},{"pmid":"28470603","id":"PMC_28470603","title":"A Generic Protocol for Purifying Disulfide-Bonded Domains and Random Protein Fragments Using Fusion Proteins with SUMO3 and Cleavage by SenP2 Protease.","date":"2017","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/28470603","citation_count":3,"is_preprint":false},{"pmid":"38916106","id":"PMC_38916106","title":"WITHDRAWN: SUMO-specific peptidase 3 mediates the SUMO3 modification of BECN1 to repress cell autophagy in gliomas.","date":"2024","source":"Histology and histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/38916106","citation_count":2,"is_preprint":false},{"pmid":"37703582","id":"PMC_37703582","title":"SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55.","date":"2023","source":"Biochemistry and cell biology = Biochimie et biologie cellulaire","url":"https://pubmed.ncbi.nlm.nih.gov/37703582","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.18.670863","title":"The C-terminal SUMOylation-dependent regulation of αKNL2 governs its centromere targeting and interaction with CENH3","date":"2025-08-21","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.18.670863","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15456,"output_tokens":4275,"usd":0.055246},"stage2":{"model":"claude-opus-4-6","input_tokens":7825,"output_tokens":3459,"usd":0.1884},"total_usd":0.243646,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"SUMO-2 and SUMO-3 contain an internal consensus SUMO modification site (ψKXE), allowing SAE1/SAE2 (E1) and Ubc9 (E2) to catalyze formation of polymeric SUMO-2 and SUMO-3 chains on protein substrates in vitro; SUMO-2 chains were also detected in vivo. This chain-forming capacity is not shared by SUMO-1.\",\n      \"method\": \"In vitro conjugation assay with purified recombinant components; in vivo detection of SUMO-2 chains; sequence analysis of ψKXE motif\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with purified components plus in vivo validation; foundational highly-cited paper (694 citations)\",\n      \"pmids\": [\"11451954\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Solution NMR structure of SUMO-3 C47S (residues 14–92) revealed a β-β-α-β-β-α-β ubiquitin fold; chemical shift perturbation mapping identified the Ubc9-binding surface on SUMO-3 as residing primarily on the hydrophilic side of the β-sheet, with negatively charged and hydrophobic residues that are electrostatically complementary to the positively charged Ubc9 surface.\",\n      \"method\": \"NMR solution structure determination; chemical shift perturbation assay for Ubc9 binding surface mapping\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — NMR structure with functional binding surface validation\",\n      \"pmids\": [\"15723523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"SUMO-3 (and SUMO-1) modifies C/EBPα at Lys159 within the synergy control (SC) motif; PIASy acts as an E3 ligase enhancing both SUMO-1 and SUMO-3 modification of C/EBPα in vivo and in vitro. SUMO modification at the SC motif limits transcriptional synergy at compound response elements, as a K159R mutation abolished SUMO modification and enhanced synergistic transactivation.\",\n      \"method\": \"In vitro SUMOylation with purified recombinant components; in vivo SUMOylation assays; site-directed mutagenesis (K159R); transcriptional reporter assays; Co-IP with Ubc9\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution plus mutagenesis plus functional transcription assay; replicated across multiple orthogonal methods\",\n      \"pmids\": [\"12511558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"C/EBPβ-1 (but not C/EBPβ-2) is conjugated by SUMO-2 and SUMO-3 at Lys173, dependent on its extreme N-terminus; mutation of Lys173 relieves C/EBPβ-1-mediated repression of the cyclin D1 promoter without altering subnuclear localization, indicating SUMO-2/3 modification mediates transcriptional repression by C/EBPβ-1.\",\n      \"method\": \"In vivo SUMOylation assay; site-directed mutagenesis (K173R); transcriptional reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean mutagenesis with functional readout, single lab\",\n      \"pmids\": [\"12810706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SUMO-3 conjugation to PML stabilizes its nuclear localization: PML is covalently modified by SUMO-3 (shown by co-IP), SUMO-3 depletion by siRNA markedly reduces PML nuclear body number and integrity (rescued by exogenous SUMO-3 but not SUMO-1 or SUMO-2), and SUMO-3 oligomerization is required for PML nuclear retention. SUMO-2 and SUMO-3 (but not SUMO-1) also localize to nucleoli.\",\n      \"method\": \"Co-immunoprecipitation; siRNA knockdown; rescue with SUMO conjugation-defective mutant; immunofluorescence localization\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus siRNA rescue experiment with specific functional readout, single lab\",\n      \"pmids\": [\"15940266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SUMO-3 enhances androgen receptor (AR) transcriptional activity in LNCaP prostate cancer cells through a mechanism independent of AR sumoylation sites and independent of SUMO-3's own conjugation function, as shown by mutational analysis of both AR sumoylation sites and SUMO-3; stable SUMO-3 overexpression enhances androgen-dependent LNCaP proliferation.\",\n      \"method\": \"Yeast functional screen; mutational analysis of AR sumoylation sites and SUMO-3 conjugation function; transcriptional reporter assay; stable overexpression; siRNA knockdown; proliferation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis plus functional reporter assay plus siRNA, single lab\",\n      \"pmids\": [\"16361251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SUMO3 (and SUMO1) modify ALS-linked SOD1 mutant proteins at Lys75 in a motoneuronal cell line; SUMO3 modification (but not SUMO1) significantly increases the stability of mutant SOD1 proteins and accelerates their intracellular aggregate formation.\",\n      \"method\": \"In vivo SUMOylation assay in motoneuronal cell line; site-directed mutagenesis of SOD1 Lys75 and Lys9; stability and aggregate formation assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis identifying specific sites plus functional aggregation assay, single lab\",\n      \"pmids\": [\"24971881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SUMO2 is essential for mouse embryonic development (Sumo2−/− embryos die ~E10.5 with severe developmental delay), while SUMO3 is dispensable (Sumo3−/− mice are viable); however, combined reduction of SUMO2 and SUMO3 (Sumo2+/−;Sumo3−/−) causes near-lethal growth defects, indicating functional redundancy and that dosage rather than isoform-specific function is critical.\",\n      \"method\": \"Genetic knockout mouse models; timed embryonic lethality analysis; compound heterozygote/null crosses\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean in vivo genetic epistasis with defined developmental phenotype, replicated across multiple genotypes\",\n      \"pmids\": [\"24891386\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Using SILAC-based quantitative proteomics after HA-SUMO3 immunoprecipitation, 188 putative SUMO3-conjugated proteins were identified in neuroblastoma cells exposed to oxygen/glucose deprivation (OGD), including transcription factors, coregulators, and PIAS2/PIAS4 ligases. Furthermore, SUMO2/3 gene silencing completely blocked OGD-induced protein ubiquitination, demonstrating crosstalk between SUMO3 conjugation and the ubiquitin pathway.\",\n      \"method\": \"SILAC quantitative proteomics; HA-SUMO3 immunoprecipitation; LC-MS/MS; siRNA gene silencing with ubiquitination readout\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MS-based interactome plus genetic silencing with defined functional crosstalk readout, single lab\",\n      \"pmids\": [\"22082260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SUMO1 and SUMO3 exert differential effects on PKR: SUMO3 expression causes PKR to concentrate around the perinuclear membrane and relocalize to nuclear dots, reduces PKR and eIF-2α activation upon viral infection or dsRNA transfection, and promotes caspase-dependent EMCV-induced PKR degradation. In contrast, SUMO1 activates PKR and eIF-2α even without viral infection.\",\n      \"method\": \"Overexpression of SUMO1 vs SUMO3; immunofluorescence localization; Western blot for PKR/eIF-2α phosphorylation; viral infection assays; caspase inhibitor experiments\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct comparison of isoforms with multiple functional readouts (localization, activation, stability), single lab\",\n      \"pmids\": [\"29352251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SUMO2 and SUMO3 (but not SUMO1) redundantly prevent a noncanonical type I interferon response; loss of sumoylation triggers spontaneous IFN production independent of IRF3, IRF7, and all known IFN-inducing pathways.\",\n      \"method\": \"Genetic loss-of-function (SUMO2 and SUMO3 knockout/knockdown); IFN production assays; epistasis with IRF3/IRF7 knockouts\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean genetic epistasis with defined pathway placement and specific phenotypic readout\",\n      \"pmids\": [\"29891701\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SUMO3 (but not SUMO1 or SUMO2) forms polymeric chains conjugated to MAVS upon poly(dA:dT) stimulation in human keratinocytes; SUMO3 chain conjugation to MAVS enhances MAVS aggregation, which drives IFN-β secretion downstream of RIG-I. Inhibition of SUMOylation (by ginkgolic acid or Ubc9 siRNA) blocked IFN-β secretion.\",\n      \"method\": \"Co-immunoprecipitation for SUMO3-MAVS conjugation; SUMO chain detection assay; Ubc9 siRNA; ginkgolic acid inhibition; IFN-β ELISA; MAVS aggregation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus functional inhibition with defined pathway outcome, single lab\",\n      \"pmids\": [\"31806367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PIAS1, together with SUMO3, mediates AR cytosolic translocation and subsequent proteasomal degradation via MDM2; AR sumoylation at Lys386 (SUMO-acceptor) and ubiquitination at Lys845 cooperate for AR nuclear export and degradation. Moreover, PIAS1 itself is modified by SUMO3 at Lys117, and this PIAS1 sumoylation is required for AR cytoplasmic redistribution and recruitment of MDM2 to drive AR ubiquitination and degradation.\",\n      \"method\": \"Immunostaining for AR localization; co-immunoprecipitation; site-directed mutagenesis (AR K386R, K845; PIAS1 K117); Western blot for ubiquitination and degradation; siRNA knockdown\",\n      \"journal\": \"Cell communication and signaling : CCS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis plus Co-IP plus localization assay with functional degradation readout, single lab\",\n      \"pmids\": [\"31752909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SUMO-3 (but not SUMO-1) promotes ubiquitin-dependent proteasomal and lysosomal degradation of TRIM55; TRIM55 contains two SUMO-interacting motifs (SIMs) that mediate this effect, as SIM-mutated TRIM55 shows increased stability, reduced polyubiquitination, and altered subcellular localization.\",\n      \"method\": \"Overexpression of SUMO-3 vs SUMO-1; SIM mutagenesis; proteasome/lysosome inhibitor assays; polyubiquitination assay; immunofluorescence microscopy\",\n      \"journal\": \"Biochemistry and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis of SIM motifs plus ubiquitination assay plus localization, single lab\",\n      \"pmids\": [\"37703582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In SUMO1-null mice, SUMO2 and/or SUMO3 compensate for SUMO1 function by sumoylating SUMO1 target proteins including RanGAP1; RanGAP1 localization is affected but PML nuclear bodies still form, demonstrating functional redundancy between SUMO isoforms in vivo.\",\n      \"method\": \"Genetic knockout mouse (SUMO1-null); immunofluorescence for RanGAP1 and PML localization; Western blot for sumoylation status\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic model with direct localization readout for SUMO1 targets\",\n      \"pmids\": [\"19033381\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SUMO3 transcription (but not SUMO2) is down-regulated by oxidative stress; Sp1 binds the Sumo3 gene promoter, and oxidative stress causes Sp1 oxidation and suppression of Sp1-DNA binding, thereby selectively reducing SUMO3 expression.\",\n      \"method\": \"qRT-PCR for SUMO2/SUMO3 mRNA; promoter characterization; chromatin immunoprecipitation (ChIP) for Sp1 binding; Sp1 oxidation assay\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP plus functional promoter analysis with direct mechanistic link, single lab\",\n      \"pmids\": [\"21291420\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SUMO3 is a ubiquitin-like modifier that, together with SUMO2 but distinct from SUMO1, forms polymeric chains via its internal ψKXE consensus site using the SAE1/SAE2 E1 and Ubc9 E2 enzymes; it covalently modifies specific substrates (including PML, C/EBPα, C/EBPβ-1, SOD1 mutants, AR, PKR, MAVS, and PIAS1) with functional consequences including regulation of nuclear localization, transcriptional synergy, protein stability and degradation, innate immune signaling (IFN-β induction via MAVS aggregation and suppression of a noncanonical IFN pathway), and antiviral responses, while its NMR solution structure reveals a ubiquitin fold with a defined negatively charged Ubc9-binding surface on the β-sheet.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SUMO3 is a ubiquitin-like post-translational modifier that conjugates to target proteins via the SAE1/SAE2 E1 and Ubc9 E2 enzymatic cascade and forms polymeric chains through an internal ψKXE consensus site, a capacity shared with SUMO2 but not SUMO1 [PMID:11451954]. SUMO3 modification regulates diverse nuclear processes including transcriptional synergy control (C/EBPα, C/EBPβ-1), PML nuclear body integrity, androgen receptor stability and degradation via PIAS1/MDM2-mediated ubiquitination, and innate immune signaling through MAVS aggregation-driven IFN-β induction and suppression of a noncanonical type I interferon response [PMID:12511558, PMID:15940266, PMID:31752909, PMID:31806367, PMID:29891701]. Although SUMO3 is largely functionally redundant with SUMO2—Sumo3-null mice are viable whereas Sumo2-null embryos die at ~E10.5—combined dosage reduction reveals essential shared roles in development, and SUMO2/3 can compensate for SUMO1 loss in modifying canonical SUMO1 substrates such as RanGAP1 [PMID:24891386, PMID:19033381]. The NMR solution structure of SUMO3 adopts a ββαββαβ ubiquitin fold, with a negatively charged β-sheet surface that mediates electrostatic recognition of Ubc9 [PMID:15723523].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing that SUMO2/3, unlike SUMO1, can form polymeric chains resolved how SUMO paralogs differ mechanistically and identified the ψKXE internal site as the basis for chain elongation via the SAE1/SAE2–Ubc9 cascade.\",\n      \"evidence\": \"In vitro reconstitution with purified E1/E2 and recombinant SUMO proteins plus in vivo chain detection\",\n      \"pmids\": [\"11451954\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No E3 ligase involvement characterized for chain formation\", \"Chain topology and length regulation undefined\", \"Functional consequences of chains vs. mono-SUMO3 not separated\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrating that SUMO3 modifies transcription factors C/EBPα and C/EBPβ-1 at specific lysines established that SUMO3 conjugation directly regulates transcriptional output—limiting synergistic transactivation (C/EBPα) and mediating transcriptional repression (C/EBPβ-1).\",\n      \"evidence\": \"In vitro and in vivo SUMOylation assays with site-directed mutagenesis (K159R, K173R) coupled to transcriptional reporter assays\",\n      \"pmids\": [\"12511558\", \"12810706\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SUMO3 at the synergy control motif attenuates transcription not defined\", \"Chromatin-level effects not examined\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"The NMR structure of SUMO3 and mapping of its Ubc9-binding surface revealed the electrostatic complementarity underlying E2 recognition, providing a structural basis for conjugation specificity.\",\n      \"evidence\": \"NMR solution structure determination with chemical shift perturbation mapping of the Ubc9 interface\",\n      \"pmids\": [\"15723523\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No co-crystal structure of the SUMO3–Ubc9 complex\", \"Structural basis for SUMO2 vs. SUMO3 discrimination by substrates not addressed\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Showing that SUMO3 is specifically required for PML nuclear body integrity—and that SUMO3 oligomerization is needed for PML nuclear retention—established a non-redundant isoform-specific role distinct from SUMO1 and SUMO2.\",\n      \"evidence\": \"siRNA depletion of SUMO3 with rescue by wild-type but not conjugation-defective SUMO3; immunofluorescence\",\n      \"pmids\": [\"15940266\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which SUMO3 chains specifically retain PML in nuclear bodies not defined\", \"Whether SUMO3 oligomerization acts via SIM-mediated interactions was not tested\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"SUMO3 enhances androgen receptor transcriptional activity and prostate cancer cell proliferation through a conjugation-independent mechanism, revealing a non-covalent function for SUMO3.\",\n      \"evidence\": \"Mutational analysis of AR sumoylation sites and SUMO3 conjugation function; reporter assay and proliferation assay in LNCaP cells\",\n      \"pmids\": [\"16361251\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Non-covalent mechanism of action uncharacterized\", \"Direct binding partner mediating conjugation-independent effect unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"In vivo compensation by SUMO2/3 for SUMO1 loss in modifying RanGAP1 demonstrated broad functional redundancy among SUMO paralogs at the organismal level.\",\n      \"evidence\": \"SUMO1-null mouse with immunofluorescence and Western blot analysis of RanGAP1 and PML sumoylation status\",\n      \"pmids\": [\"19033381\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which E3 ligases redirect SUMO2/3 to SUMO1 targets not identified\", \"Whether compensatory modification is qualitatively equivalent unclear\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Proteomic identification of 188 SUMO3 substrates under ischemia and the finding that SUMO2/3 silencing blocks stress-induced ubiquitination established a direct crosstalk between the SUMO3 and ubiquitin pathways under cellular stress.\",\n      \"evidence\": \"SILAC-based quantitative proteomics with HA-SUMO3 IP in neuroblastoma cells; siRNA-mediated SUMO2/3 depletion with ubiquitination readout\",\n      \"pmids\": [\"22082260\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Individual SUMO3 substrates not validated by orthogonal methods\", \"Molecular link between SUMO3 conjugation and ubiquitin ligase recruitment not identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Selective transcriptional downregulation of SUMO3 (but not SUMO2) by oxidative stress through Sp1 oxidation revealed that SUMO3 abundance is dynamically regulated, providing a mechanism for stress-dependent shifts in the SUMO2/3 ratio.\",\n      \"evidence\": \"qRT-PCR, promoter analysis, and ChIP for Sp1 binding under oxidative stress\",\n      \"pmids\": [\"21291420\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether reduced SUMO3 alters the poly-SUMO chain landscape under stress not tested\", \"Sp1 oxidation site not mapped\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Genetic analysis in mice established that SUMO3 is individually dispensable for viability but becomes essential in combination with reduced SUMO2, proving dosage-dependent functional redundancy rather than strict isoform-specific roles in development.\",\n      \"evidence\": \"Sumo2 and Sumo3 single and compound knockout mice; timed embryonic analysis\",\n      \"pmids\": [\"24891386\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific developmental processes requiring SUMO2/3 dosage not identified\", \"Whether tissue-specific expression differences contribute to the dosage requirement unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"SUMO2/3 were shown to actively suppress a noncanonical type I interferon response independent of known IFN-inducing pathways, positioning SUMOylation as a constitutive checkpoint on innate immune activation.\",\n      \"evidence\": \"SUMO2/3 genetic knockout combined with epistasis analysis using IRF3/IRF7 knockouts; IFN production assays\",\n      \"pmids\": [\"29891701\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the SUMO2/3-modified target(s) that suppress noncanonical IFN unknown\", \"Whether this reflects mono- vs. poly-SUMO modification not determined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"SUMO3 poly-chain conjugation to MAVS was shown to drive MAVS aggregation and IFN-β production in response to cytosolic DNA sensing, establishing a direct mechanistic link between SUMO3 chains and innate antiviral signaling.\",\n      \"evidence\": \"Co-IP of SUMO3-MAVS; MAVS aggregation assay; Ubc9 siRNA and ginkgolic acid inhibition; IFN-β ELISA in keratinocytes\",\n      \"pmids\": [\"31806367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SUMO3 conjugation sites on MAVS not mapped\", \"E3 ligase mediating MAVS SUMO3 modification not identified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"SUMO3 modification of PIAS1 at K117 was shown to be required for AR cytoplasmic redistribution and MDM2-mediated AR ubiquitination and proteasomal degradation, establishing a SUMO3→ubiquitin→degradation cascade for AR.\",\n      \"evidence\": \"Site-directed mutagenesis of PIAS1 K117 and AR K386/K845; Co-IP; AR localization by immunostaining; degradation assays\",\n      \"pmids\": [\"31752909\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether SUMO3 modification of PIAS1 alters its E3 ligase activity broadly or is AR-specific unknown\", \"In vivo relevance in prostate tissue not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating that SUMO3 promotes TRIM55 degradation through SIM-dependent ubiquitination via both proteasomal and lysosomal routes generalized the SUMO3-to-ubiquitin degradation mechanism to a non-covalent (SIM-mediated) mode of action.\",\n      \"evidence\": \"SUMO3 overexpression; SIM mutagenesis in TRIM55; proteasome and lysosome inhibitor assays; polyubiquitination assay\",\n      \"pmids\": [\"37703582\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether SUMO3 acts as a direct bridging factor or recruits a SUMO-targeted ubiquitin ligase (STUbL) for TRIM55 degradation not determined\", \"Physiological context of TRIM55–SUMO3 interaction not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the identity of SUMO3-specific substrates vs. shared SUMO2/3 substrates at endogenous expression levels, the E3 ligases and deconjugases that confer SUMO3 specificity in innate immune signaling, and the structural basis for differential recognition of SUMO3 chains by SIM-containing effectors.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No systematic endogenous-level SUMO3-specific substrate catalog exists\", \"SUMO3 chain readers/decoders not comprehensively identified\", \"No structural model of a SUMO3 poly-chain bound to a SIM-containing effector\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [0, 2, 3, 4, 6, 11, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4, 9]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2, 3, 8, 12, 13]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [10, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [2, 3, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"UBC9\",\n      \"PML\",\n      \"MAVS\",\n      \"PIAS1\",\n      \"PIASy\",\n      \"AR\",\n      \"CEBPA\",\n      \"CEBPB\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}