{"gene":"PF3D7_0527100","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":2007,"finding":"PF3D7_0527100 (UBC13) is a substrate of the P. falciparum kinase PfPK9; PfPK9 phosphorylates UBC13 at S106, a conserved residue among eukaryotic E2 ubiquitin-conjugating enzymes, and this phosphorylation suppresses UBC13's ubiquitin-conjugating activity in vitro.","method":"In vitro kinase assay with recombinant PfPK9 and UBC13, phosphopeptide mapping identifying S106 as phosphorylation site, ubiquitin-conjugating activity assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay with site-specific mutagenesis/mapping and functional readout (suppressed ubiquitin-conjugating activity); single lab but multiple orthogonal methods","pmids":["17452636"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"PF3D7_0527100 (UBC13) mediates K63-linkage-specific polyubiquitination in P. falciparum; inhibition of PfPK9 (which phosphorylates UBC13) with small molecules takinib or HS220 decreases K63-linked ubiquitination in parasite cells.","method":"Chemical inhibition of PfPK9 (takinib, HS220) in P. falciparum followed by quantification of K63-linked ubiquitination by immunoblot","journal":"Cell chemical biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — K63-Ub reduction shown in cells with selective inhibitor, but indirect (via PfPK9 inhibition) and single lab","pmids":["30595530"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"In P. berghei, phosphorylation of UBC13 at regulatory S106 is essential for blood-stage parasite viability; however, PbPK9 is dispensable for this phosphorylation (phosphorylation of S106 still occurs in PK9 knockout parasites), demonstrating redundancy in the kinase(s) responsible for this modification. UBC13 and PK9 co-localize in the cytosol of erythrocytic and liver stages.","method":"Genetic knockout of PK9 in P. berghei, site-directed mutation of UBC13 S106, phosphorylation analysis, co-localization by immunofluorescence, parasite viability assays across life cycle stages","journal":"Microbiological research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean genetic KO with defined viability phenotype and phosphorylation analysis, single lab","pmids":["35490588"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2021,"finding":"Deletion of UBC13 (PF3D7_0527100) in P. falciparum reduces K63-linked ubiquitination of protein substrates, impairs asexual blood-stage parasite growth in vitro, and increases parasite sensitivity to the DNA mutagen methyl methanesulfonate and to dihydroartemisinin (but not chloroquine), establishing UBC13 as the E2 enzyme responsible for K63-ubiquitylation and implicating this pathway in DNA repair and artemisinin response.","method":"Inducible Di-Cre genetic deletion of ubc13 in P. falciparum, K63-Ub immunoblot, in vitro growth assay, drug sensitivity assays (MMS, DHA, chloroquine), chemical inhibition with NSC697923","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean inducible KO with multiple orthogonal functional readouts (K63-Ub reduction, growth, drug sensitivity), single lab","pmids":["34750454"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PF3D7_0527100 (UBC13) is an E3 ligase-interacting E2 enzyme; the P. falciparum RBR-E3 ligase physically interacts with UBC13 (and UBCH5) as shown by immunoprecipitation, and the E3 catalyzes K6, K11, K48, and K63-mediated polyubiquitination.","method":"Co-immunoprecipitation of Pf RBR-E3 ligase with UBC13 in P. falciparum","journal":"Proteins","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-IP experiment, single lab, no reciprocal pulldown or functional validation of the UBC13-RBR interaction specifically","pmids":["40035193"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"NSC697923 covalently targets the catalytic cysteine of PF3D7_0527100 (UBC13) with nanomolar inhibitory potency, specifically reduces K63-linked ubiquitination in blood-stage P. falciparum, and chemoproteomic profiling identified 31 putative UBC13 substrates enriched in transcription, translation, and proteasome processes. Inhibition of UBC13 reduces nascent protein synthesis, establishing a role for UBC13-dependent K63-ubiquitination in protein translation. NSC697923 synergizes with dihydroartemisinin.","method":"Covalent inhibitor characterization (NSC697923), in vitro inhibitory potency assay, K63-Ub immunoblot in parasites, chemoproteomic substrate identification (31 substrates), nascent protein synthesis assay (puromycin incorporation or similar), drug synergy assay","journal":"iScience","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — catalytic cysteine covalent targeting demonstrated biochemically, K63-Ub reduction in cells, chemoproteomic substrate identification, and functional translation readout; multiple orthogonal methods in single study","pmids":["40491475"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0527100 (UBC13) is a ubiquitin-conjugating enzyme that catalyzes K63-linked polyubiquitination in P. falciparum via its catalytic cysteine; its activity is negatively regulated by phosphorylation at S106 (mediated by PfPK9 in P. falciparum, though redundant kinases compensate in P. berghei), it is essential for blood-stage parasite growth and DNA repair, and K63-ubiquitination by UBC13 supports protein translation; UBC13 also physically interacts with the P. falciparum RBR-E3 ligase and its inhibition synergizes with dihydroartemisinin."},"narrative":{"mechanistic_narrative":"PF3D7_0527100 (UBC13) is the ubiquitin-conjugating (E2) enzyme responsible for K63-linkage-specific polyubiquitination in Plasmodium falciparum, and this activity is essential for asexual blood-stage growth [PMID:34750454]. Genetic deletion of ubc13 reduces cellular K63-linked ubiquitination, impairs parasite proliferation, and sensitizes parasites to the DNA mutagen methyl methanesulfonate and to dihydroartemisinin but not chloroquine, linking UBC13-dependent K63-ubiquitination to DNA repair and artemisinin response [PMID:34750454]. Catalysis depends on the enzyme's catalytic cysteine, which is covalently and potently targeted by the inhibitor NSC697923; inhibition selectively lowers K63-ubiquitination, reduces nascent protein synthesis, and identifies UBC13 substrates enriched in transcription, translation, and proteasome-associated processes, extending its role to protein translation [PMID:40491475]. UBC13 activity is negatively regulated by phosphorylation at the conserved residue S106, which suppresses its ubiquitin-conjugating activity in vitro [PMID:17452636]; in P. falciparum this modification is mediated by the kinase PfPK9 [PMID:17452636, PMID:30595530], whereas in P. berghei S106 phosphorylation is essential for blood-stage viability but occurs independently of PbPK9, indicating redundant kinase activity [PMID:35490588]. UBC13 physically associates with the P. falciparum RBR-E3 ligase [PMID:40035193].","teleology":[{"year":2007,"claim":"Establishing how UBC13 activity is controlled, this work identified UBC13 as a phospho-substrate whose conjugating activity is switched off by modification of a conserved E2 residue.","evidence":"In vitro kinase assay with recombinant PfPK9 and UBC13, phosphopeptide mapping to S106, and ubiquitin-conjugating activity assay","pmids":["17452636"],"confidence":"High","gaps":["In vitro only; cellular consequences of S106 phosphorylation not tested","Whether phosphorylation blocks E2 charging or thioester transfer not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"Connecting UBC13 regulation to a specific ubiquitin output, chemical inhibition of its upstream kinase reduced K63-linked ubiquitination in living parasites, tying UBC13 to K63 chain formation in cells.","evidence":"Chemical inhibition of PfPK9 (takinib, HS220) in P. falciparum with K63-Ub immunoblot readout","pmids":["30595530"],"confidence":"Medium","gaps":["Effect on K63-Ub is indirect, inferred through PfPK9 inhibition rather than direct UBC13 perturbation","Kinase inhibitors may have off-target effects on other substrates"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"Directly testing UBC13's cellular role, inducible deletion established it as the E2 enzyme driving K63-ubiquitination and required for blood-stage growth, DNA repair, and artemisinin sensitivity.","evidence":"Inducible Di-Cre deletion of ubc13 in P. falciparum with K63-Ub immunoblot, growth and drug-sensitivity (MMS, DHA, chloroquine) assays, and chemical inhibition (NSC697923)","pmids":["34750454"],"confidence":"High","gaps":["Substrates whose K63-ubiquitination mediates DNA repair not identified","Mechanism linking K63-ubiquitination to DHA response unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"Assessing kinase specificity in vivo, a P. berghei knockout showed S106 phosphorylation is essential for viability yet occurs independently of PbPK9, revealing kinase redundancy for this regulatory mark.","evidence":"PK9 knockout in P. berghei, site-directed mutation of UBC13 S106, phosphorylation analysis, immunofluorescence co-localization, and life-cycle viability assays","pmids":["35490588"],"confidence":"Medium","gaps":["Identity of the redundant kinase(s) phosphorylating S106 unknown","Species divergence from P. falciparum PfPK9 dependence not mechanistically explained"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"claim":"Pinpointing the catalytic requirement and downstream biology, covalent targeting of the catalytic cysteine defined UBC13's substrate landscape and revealed a role in translation, with therapeutic synergy against DHA.","evidence":"Covalent inhibitor (NSC697923) characterization, in vitro potency, parasite K63-Ub immunoblot, chemoproteomic substrate identification (31 substrates), nascent protein synthesis assay, and DHA synergy assay in P. falciparum","pmids":["40491475"],"confidence":"High","gaps":["Which of the 31 putative substrates are direct, physiologically K63-ubiquitinated targets not validated individually","Mechanism by which K63-ubiquitination promotes translation not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Placing UBC13 in an E2-E3 pairing, co-immunoprecipitation showed physical association with the P. falciparum RBR-E3 ligase capable of multiple ubiquitin linkages.","evidence":"Co-immunoprecipitation of Pf RBR-E3 ligase with UBC13 in P. falciparum","pmids":["40035193"],"confidence":"Low","gaps":["Single co-IP without reciprocal pulldown or functional validation of the UBC13-RBR interaction","Whether UBC13 cooperates with this E3 to build K63 chains specifically not shown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The physiological substrates whose K63-ubiquitination by UBC13 drives DNA repair, translation, and artemisinin response, and the identity of the redundant S106 kinase(s), remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No validated direct substrate list for UBC13-dependent K63 chains","Cognate E3 ligase(s) partnering UBC13 for each cellular output not established","Structural basis for S106 phospho-regulation of catalysis unknown"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFPK9 (KINASE PHOSPHORYLATING UBC13 S106 IN P. FALCIPARUM)","PF RBR-E3 LIGASE (CO-IP INTERACTOR)"],"other_free_text":["Activity negatively regulated by phosphorylation at conserved residue S106 [#0]; PfPK9-dependent in P. falciparum but PbPK9-independent (redundant kinases) in P. berghei [#2].","Catalytic cysteine covalently targeted by NSC697923 with nanomolar potency [#5].","Deletion or inhibition sensitizes parasites to methyl methanesulfonate and dihydroartemisinin (not chloroquine); NSC697923 synergizes with dihydroartemisinin [#3, #5].","Chemoproteomics identified 31 putative substrates enriched in transcription, translation, and proteasome processes [#5]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"17452636","id":"PMC_17452636","title":"Characterization of a UBC13 kinase in Plasmodium falciparum.","date":"2007","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/17452636","citation_count":25,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UBC13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"30595530","id":"PMC_30595530","title":"Plasmodium PK9 Inhibitors Promote Growth of Liver-Stage Parasites.","date":"2018","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/30595530","citation_count":14,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfUBC13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35490588","id":"PMC_35490588","title":"Protein kinase 9 is not required for completion of the Plasmodium berghei life cycle.","date":"2022","source":"Microbiological research","url":"https://pubmed.ncbi.nlm.nih.gov/35490588","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UBC13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34750454","id":"PMC_34750454","title":"Deletion of Plasmodium falciparum ubc13 increases parasite sensitivity to the mutagen, methyl methanesulfonate and dihydroartemisinin.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/34750454","citation_count":9,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UBC13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40035193","id":"PMC_40035193","title":"Understanding the Role of RING-Between-RING E3 Ligase of the Human Malaria Parasite.","date":"2025","source":"Proteins","url":"https://pubmed.ncbi.nlm.nih.gov/40035193","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UBC13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40491475","id":"PMC_40491475","title":"Covalent inhibition of Plasmodium falciparum Ubc13 impairs global protein synthesis.","date":"2025","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/40491475","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UBC13","PfUBC13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5575,"output_tokens":2046,"usd":0.023707,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7195,"output_tokens":3249,"usd":0.0586,"stage2_stop_reason":"end_turn"},"total_usd":0.082307,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"PF3D7_0527100 (UBC13) is a substrate of the P. falciparum kinase PfPK9; PfPK9 phosphorylates UBC13 at S106, a conserved residue among eukaryotic E2 ubiquitin-conjugating enzymes, and this phosphorylation suppresses UBC13's ubiquitin-conjugating activity in vitro.\",\n      \"method\": \"In vitro kinase assay with recombinant PfPK9 and UBC13, phosphopeptide mapping identifying S106 as phosphorylation site, ubiquitin-conjugating activity assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay with site-specific mutagenesis/mapping and functional readout (suppressed ubiquitin-conjugating activity); single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17452636\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PF3D7_0527100 (UBC13) mediates K63-linkage-specific polyubiquitination in P. falciparum; inhibition of PfPK9 (which phosphorylates UBC13) with small molecules takinib or HS220 decreases K63-linked ubiquitination in parasite cells.\",\n      \"method\": \"Chemical inhibition of PfPK9 (takinib, HS220) in P. falciparum followed by quantification of K63-linked ubiquitination by immunoblot\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — K63-Ub reduction shown in cells with selective inhibitor, but indirect (via PfPK9 inhibition) and single lab\",\n      \"pmids\": [\"30595530\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In P. berghei, phosphorylation of UBC13 at regulatory S106 is essential for blood-stage parasite viability; however, PbPK9 is dispensable for this phosphorylation (phosphorylation of S106 still occurs in PK9 knockout parasites), demonstrating redundancy in the kinase(s) responsible for this modification. UBC13 and PK9 co-localize in the cytosol of erythrocytic and liver stages.\",\n      \"method\": \"Genetic knockout of PK9 in P. berghei, site-directed mutation of UBC13 S106, phosphorylation analysis, co-localization by immunofluorescence, parasite viability assays across life cycle stages\",\n      \"journal\": \"Microbiological research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean genetic KO with defined viability phenotype and phosphorylation analysis, single lab\",\n      \"pmids\": [\"35490588\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Deletion of UBC13 (PF3D7_0527100) in P. falciparum reduces K63-linked ubiquitination of protein substrates, impairs asexual blood-stage parasite growth in vitro, and increases parasite sensitivity to the DNA mutagen methyl methanesulfonate and to dihydroartemisinin (but not chloroquine), establishing UBC13 as the E2 enzyme responsible for K63-ubiquitylation and implicating this pathway in DNA repair and artemisinin response.\",\n      \"method\": \"Inducible Di-Cre genetic deletion of ubc13 in P. falciparum, K63-Ub immunoblot, in vitro growth assay, drug sensitivity assays (MMS, DHA, chloroquine), chemical inhibition with NSC697923\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean inducible KO with multiple orthogonal functional readouts (K63-Ub reduction, growth, drug sensitivity), single lab\",\n      \"pmids\": [\"34750454\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PF3D7_0527100 (UBC13) is an E3 ligase-interacting E2 enzyme; the P. falciparum RBR-E3 ligase physically interacts with UBC13 (and UBCH5) as shown by immunoprecipitation, and the E3 catalyzes K6, K11, K48, and K63-mediated polyubiquitination.\",\n      \"method\": \"Co-immunoprecipitation of Pf RBR-E3 ligase with UBC13 in P. falciparum\",\n      \"journal\": \"Proteins\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-IP experiment, single lab, no reciprocal pulldown or functional validation of the UBC13-RBR interaction specifically\",\n      \"pmids\": [\"40035193\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NSC697923 covalently targets the catalytic cysteine of PF3D7_0527100 (UBC13) with nanomolar inhibitory potency, specifically reduces K63-linked ubiquitination in blood-stage P. falciparum, and chemoproteomic profiling identified 31 putative UBC13 substrates enriched in transcription, translation, and proteasome processes. Inhibition of UBC13 reduces nascent protein synthesis, establishing a role for UBC13-dependent K63-ubiquitination in protein translation. NSC697923 synergizes with dihydroartemisinin.\",\n      \"method\": \"Covalent inhibitor characterization (NSC697923), in vitro inhibitory potency assay, K63-Ub immunoblot in parasites, chemoproteomic substrate identification (31 substrates), nascent protein synthesis assay (puromycin incorporation or similar), drug synergy assay\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — catalytic cysteine covalent targeting demonstrated biochemically, K63-Ub reduction in cells, chemoproteomic substrate identification, and functional translation readout; multiple orthogonal methods in single study\",\n      \"pmids\": [\"40491475\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0527100 (UBC13) is a ubiquitin-conjugating enzyme that catalyzes K63-linked polyubiquitination in P. falciparum via its catalytic cysteine; its activity is negatively regulated by phosphorylation at S106 (mediated by PfPK9 in P. falciparum, though redundant kinases compensate in P. berghei), it is essential for blood-stage parasite growth and DNA repair, and K63-ubiquitination by UBC13 supports protein translation; UBC13 also physically interacts with the P. falciparum RBR-E3 ligase and its inhibition synergizes with dihydroartemisinin.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0527100 (UBC13) is the ubiquitin-conjugating (E2) enzyme responsible for K63-linkage-specific polyubiquitination in Plasmodium falciparum, and this activity is essential for asexual blood-stage growth [#3]. Genetic deletion of ubc13 reduces cellular K63-linked ubiquitination, impairs parasite proliferation, and sensitizes parasites to the DNA mutagen methyl methanesulfonate and to dihydroartemisinin but not chloroquine, linking UBC13-dependent K63-ubiquitination to DNA repair and artemisinin response [#3]. Catalysis depends on the enzyme's catalytic cysteine, which is covalently and potently targeted by the inhibitor NSC697923; inhibition selectively lowers K63-ubiquitination, reduces nascent protein synthesis, and identifies UBC13 substrates enriched in transcription, translation, and proteasome-associated processes, extending its role to protein translation [#5]. UBC13 activity is negatively regulated by phosphorylation at the conserved residue S106, which suppresses its ubiquitin-conjugating activity in vitro [#0]; in P. falciparum this modification is mediated by the kinase PfPK9 [#0, #1], whereas in P. berghei S106 phosphorylation is essential for blood-stage viability but occurs independently of PbPK9, indicating redundant kinase activity [#2]. UBC13 physically associates with the P. falciparum RBR-E3 ligase [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing how UBC13 activity is controlled, this work identified UBC13 as a phospho-substrate whose conjugating activity is switched off by modification of a conserved E2 residue.\",\n      \"evidence\": \"In vitro kinase assay with recombinant PfPK9 and UBC13, phosphopeptide mapping to S106, and ubiquitin-conjugating activity assay\",\n      \"pmids\": [\"17452636\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"In vitro only; cellular consequences of S106 phosphorylation not tested\",\n        \"Whether phosphorylation blocks E2 charging or thioester transfer not resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Connecting UBC13 regulation to a specific ubiquitin output, chemical inhibition of its upstream kinase reduced K63-linked ubiquitination in living parasites, tying UBC13 to K63 chain formation in cells.\",\n      \"evidence\": \"Chemical inhibition of PfPK9 (takinib, HS220) in P. falciparum with K63-Ub immunoblot readout\",\n      \"pmids\": [\"30595530\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Effect on K63-Ub is indirect, inferred through PfPK9 inhibition rather than direct UBC13 perturbation\",\n        \"Kinase inhibitors may have off-target effects on other substrates\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Directly testing UBC13's cellular role, inducible deletion established it as the E2 enzyme driving K63-ubiquitination and required for blood-stage growth, DNA repair, and artemisinin sensitivity.\",\n      \"evidence\": \"Inducible Di-Cre deletion of ubc13 in P. falciparum with K63-Ub immunoblot, growth and drug-sensitivity (MMS, DHA, chloroquine) assays, and chemical inhibition (NSC697923)\",\n      \"pmids\": [\"34750454\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Substrates whose K63-ubiquitination mediates DNA repair not identified\",\n        \"Mechanism linking K63-ubiquitination to DHA response unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Assessing kinase specificity in vivo, a P. berghei knockout showed S106 phosphorylation is essential for viability yet occurs independently of PbPK9, revealing kinase redundancy for this regulatory mark.\",\n      \"evidence\": \"PK9 knockout in P. berghei, site-directed mutation of UBC13 S106, phosphorylation analysis, immunofluorescence co-localization, and life-cycle viability assays\",\n      \"pmids\": [\"35490588\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Identity of the redundant kinase(s) phosphorylating S106 unknown\",\n        \"Species divergence from P. falciparum PfPK9 dependence not mechanistically explained\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Pinpointing the catalytic requirement and downstream biology, covalent targeting of the catalytic cysteine defined UBC13's substrate landscape and revealed a role in translation, with therapeutic synergy against DHA.\",\n      \"evidence\": \"Covalent inhibitor (NSC697923) characterization, in vitro potency, parasite K63-Ub immunoblot, chemoproteomic substrate identification (31 substrates), nascent protein synthesis assay, and DHA synergy assay in P. falciparum\",\n      \"pmids\": [\"40491475\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Which of the 31 putative substrates are direct, physiologically K63-ubiquitinated targets not validated individually\",\n        \"Mechanism by which K63-ubiquitination promotes translation not defined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placing UBC13 in an E2-E3 pairing, co-immunoprecipitation showed physical association with the P. falciparum RBR-E3 ligase capable of multiple ubiquitin linkages.\",\n      \"evidence\": \"Co-immunoprecipitation of Pf RBR-E3 ligase with UBC13 in P. falciparum\",\n      \"pmids\": [\"40035193\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single co-IP without reciprocal pulldown or functional validation of the UBC13-RBR interaction\",\n        \"Whether UBC13 cooperates with this E3 to build K63 chains specifically not shown\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The physiological substrates whose K63-ubiquitination by UBC13 drives DNA repair, translation, and artemisinin response, and the identity of the redundant S106 kinase(s), remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No validated direct substrate list for UBC13-dependent K63 chains\",\n        \"Cognate E3 ligase(s) partnering UBC13 for each cellular output not established\",\n        \"Structural basis for S106 phospho-regulation of catalysis unknown\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0061631\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"GO:0070534\", \"supporting_discovery_ids\": [1, 3, 5]},\n      {\"term_id\": \"GO:0031436\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0070534\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0006281\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0016567\", \"supporting_discovery_ids\": [0, 3, 4, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfPK9 (kinase phosphorylating UBC13 S106 in P. falciparum)\",\n      \"Pf RBR-E3 ligase (co-IP interactor)\"\n    ],\n    \"other_free_text\": [\n      \"Activity negatively regulated by phosphorylation at conserved residue S106 [#0]; PfPK9-dependent in P. falciparum but PbPK9-independent (redundant kinases) in P. berghei [#2].\",\n      \"Catalytic cysteine covalently targeted by NSC697923 with nanomolar potency [#5].\",\n      \"Deletion or inhibition sensitizes parasites to methyl methanesulfonate and dihydroartemisinin (not chloroquine); NSC697923 synergizes with dihydroartemisinin [#3, #5].\",\n      \"Chemoproteomics identified 31 putative substrates enriched in transcription, translation, and proteasome processes [#5].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0527100","name":null,"product":"ubiquitin-conjugating enzyme E2 13","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1241900","name":null,"product":"ubiquitin-conjugating enzyme E2 N, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1005600","name":null,"product":"ubiquitin-conjugating enzyme E2 13, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"UBC13","evaluation":null}