{"gene":"PF3D7_0305700","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2015,"finding":"The P. falciparum SUMO E2-conjugating enzyme (PF3D7_0305700/PfUbc9) interacts with the P. falciparum SUMO E1-activating enzyme via surface residues that are distinct from the human E1-E2 interface, as determined by x-ray crystallography of the human E1 ubiquitin fold domain–Ubc9 complex combined with in silico modeling, mutagenesis, and in vitro biochemical studies of the P. falciparum enzymes.","method":"X-ray crystallography, in silico modeling, site-directed mutagenesis, in vitro biochemical assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus mutagenesis plus in vitro biochemical validation in a single rigorous study","pmids":["26697886"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"SUMOylation (in which PF3D7_0305700/PfUbc9 functions as the E2-conjugating enzyme) plays a protective role in P. falciparum asexual trophozoite stages under iron-induced oxidative stress, as evidenced by the parasite's susceptibility to oxidative stress correlating with SUMOylation pathway activity.","method":"Cell-based oxidative stress assays on asexual blood-stage P. falciparum","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, indirect functional readout linking SUMOylation pathway to oxidative stress without direct genetic perturbation of PF3D7_0305700","pmids":["26697886"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"A unidirectional cross-species interaction exists in the SUMO conjugation system: Pf-SUMO can interact with human E2 (Ubc9), but Hs-SUMO1 fails to interact with Pf-E2 (PF3D7_0305700). Critical residues at the N-terminus of Pf-E2/PF3D7_0305700 are responsible for the diminished Hs-SUMO1–Pf-E2 interaction; mutating these to the corresponding Hs-Ubc9 residues restores cross-species interaction by re-establishing electrostatic, π-π, and hydrophobic interactions.","method":"Biochemical and biophysical interaction analyses, site-directed mutagenesis","journal":"Biophysical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction tests with mutagenesis and biophysical validation in a single lab","pmids":["35331687"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PF3D7_0305700 was captured as an active E2 ubiquitin-conjugating enzyme by a ubiquitin activity-based probe (Ub-Dha) during P. falciparum asexual blood-stage development, and was validated through in vitro ubiquitination assays; it was also shown to have selective functional interactions with the HECT E3 ligase PfHEUL.","method":"Activity-based protein profiling (Ub-Dha probe), in vitro ubiquitination assays","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — activity-based probe capture plus in vitro assay validation, single lab, single study","pmids":["40249735"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0305700 is an active E2 ubiquitin/SUMO-conjugating enzyme in P. falciparum that engages the SUMO E1-activating enzyme through species-specific surface residues (distinct from the human interface), interacts selectively with the HECT E3 ligase PfHEUL in ubiquitin transfer, and contributes to parasite survival under oxidative stress during asexual blood-stage development."},"narrative":{"mechanistic_narrative":"PF3D7_0305700 is an active E2-conjugating enzyme of Plasmodium falciparum that operates in both the SUMO and ubiquitin conjugation systems during asexual blood-stage development [PMID:26697886, PMID:40249735]. In the SUMO pathway, it functions as the E2-conjugating enzyme that engages the P. falciparum SUMO E1-activating enzyme through surface residues distinct from the human E1–E2 interface [PMID:26697886], and this SUMOylation activity contributes to protecting trophozoite-stage parasites against iron-induced oxidative stress [PMID:26697886]. The parasite enzyme also displays species-specific SUMO recognition: whereas Pf-SUMO can engage human E2, Hs-SUMO1 fails to interact with PF3D7_0305700, a selectivity governed by critical N-terminal residues whose mutation to the human counterparts restores the cross-species interaction [PMID:35331687]. In the ubiquitin pathway, PF3D7_0305700 was captured as a catalytically active E2 by a ubiquitin activity-based probe and validated in vitro, and it shows selective functional interaction with the HECT E3 ligase PfHEUL [PMID:40249735]. Beyond these activities, the enzyme's full substrate repertoire and its in vivo genetic requirement remain uncharacterized in the available corpus.","teleology":[{"year":2015,"claim":"Establishing how the parasite SUMO E2 engages its E1 partner was needed to define whether the conjugation interface diverges from the human system and could be selectively targeted; crystallography plus mutagenesis showed the P. falciparum E1–E2 interaction uses surface residues distinct from the human interface.","evidence":"X-ray crystallography of the human E1 ubiquitin fold domain–Ubc9 complex with in silico modeling, site-directed mutagenesis, and in vitro biochemistry of the P. falciparum enzymes","pmids":["26697886"],"confidence":"High","gaps":["No crystal structure of the P. falciparum E1–E2 complex itself","SUMO substrates conjugated via this E2 not identified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"It was unclear whether SUMOylation had a defined physiological role in blood-stage parasites; oxidative-stress assays linked SUMOylation pathway activity, in which PF3D7_0305700 acts as the E2, to protection of trophozoites under iron-induced oxidative stress.","evidence":"Cell-based oxidative stress assays on asexual blood-stage P. falciparum","pmids":["26697886"],"confidence":"Medium","gaps":["Indirect readout without direct genetic perturbation of PF3D7_0305700","Protective mechanism and relevant SUMOylated targets undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"To determine the structural basis of SUMO recognition specificity, cross-species interaction tests asked whether parasite and human components are interchangeable; they revealed a unidirectional interaction in which Hs-SUMO1 fails to engage PF3D7_0305700 owing to critical N-terminal residues, restorable by humanizing those residues.","evidence":"Biochemical and biophysical interaction analyses with site-directed mutagenesis and reciprocal cross-species interaction tests","pmids":["35331687"],"confidence":"Medium","gaps":["Consequences of the specificity for in vivo SUMO conjugation not tested","Single-lab biophysical characterization"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether PF3D7_0305700 also acts as a bona fide ubiquitin E2 in living parasites was open; activity-based probe capture during blood-stage growth plus in vitro ubiquitination confirmed it as an active ubiquitin-conjugating enzyme with selective interaction with the HECT E3 PfHEUL.","evidence":"Activity-based protein profiling with a Ub-Dha probe during P. falciparum asexual development and in vitro ubiquitination assays","pmids":["40249735"],"confidence":"Medium","gaps":["Ubiquitination substrates and chain topology not defined","Functional consequence of the PfHEUL interaction in vivo untested","Single study, single lab"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether PF3D7_0305700 is genetically essential and what its physiological substrate set is across the SUMO and ubiquitin pathways in the intact parasite.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No conditional knockdown or knockout phenotype reported","No in vivo substrate identification","Relative contribution of SUMO versus ubiquitin conjugation roles undetermined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["P. FALCIPARUM SUMO E1-ACTIVATING ENZYME [#0]","PF-SUMO [#2]","PFHEUL (HECT E3 LIGASE) [#3]"],"other_free_text":["Engages the SUMO E1 via surface residues distinct from the human E1–E2 interface [#0].","Species-specific SUMO recognition governed by N-terminal residues; humanizing these restores Hs-SUMO1 interaction [#2].","Captured as an active E2 by a ubiquitin activity-based probe (Ub-Dha) during asexual blood-stage development [#3].","SUMOylation activity is protective under iron-induced oxidative stress in trophozoites [#1]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"26697886","id":"PMC_26697886","title":"Characterization and Structural Insights into Selective E1-E2 Interactions in the Human and Plasmodium falciparum SUMO Conjugation Systems.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26697886","citation_count":14,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ubiquitin-conjugating enzyme E2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35331687","id":"PMC_35331687","title":"Implications of critical node-dependent unidirectional cross-talk of Plasmodium SUMO pathway proteins.","date":"2022","source":"Biophysical journal","url":"https://pubmed.ncbi.nlm.nih.gov/35331687","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfE2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40249735","id":"PMC_40249735","title":"Activity-based protein profiling reveals both canonical and novel ubiquitin pathway enzymes in Plasmodium.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/40249735","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4185,"output_tokens":1261,"usd":0.015735,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6080,"output_tokens":2380,"usd":0.04495,"stage2_stop_reason":"end_turn"},"total_usd":0.060685,"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\": 2015,\n      \"finding\": \"The P. falciparum SUMO E2-conjugating enzyme (PF3D7_0305700/PfUbc9) interacts with the P. falciparum SUMO E1-activating enzyme via surface residues that are distinct from the human E1-E2 interface, as determined by x-ray crystallography of the human E1 ubiquitin fold domain–Ubc9 complex combined with in silico modeling, mutagenesis, and in vitro biochemical studies of the P. falciparum enzymes.\",\n      \"method\": \"X-ray crystallography, in silico modeling, site-directed mutagenesis, in vitro biochemical assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus mutagenesis plus in vitro biochemical validation in a single rigorous study\",\n      \"pmids\": [\"26697886\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SUMOylation (in which PF3D7_0305700/PfUbc9 functions as the E2-conjugating enzyme) plays a protective role in P. falciparum asexual trophozoite stages under iron-induced oxidative stress, as evidenced by the parasite's susceptibility to oxidative stress correlating with SUMOylation pathway activity.\",\n      \"method\": \"Cell-based oxidative stress assays on asexual blood-stage P. falciparum\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, indirect functional readout linking SUMOylation pathway to oxidative stress without direct genetic perturbation of PF3D7_0305700\",\n      \"pmids\": [\"26697886\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A unidirectional cross-species interaction exists in the SUMO conjugation system: Pf-SUMO can interact with human E2 (Ubc9), but Hs-SUMO1 fails to interact with Pf-E2 (PF3D7_0305700). Critical residues at the N-terminus of Pf-E2/PF3D7_0305700 are responsible for the diminished Hs-SUMO1–Pf-E2 interaction; mutating these to the corresponding Hs-Ubc9 residues restores cross-species interaction by re-establishing electrostatic, π-π, and hydrophobic interactions.\",\n      \"method\": \"Biochemical and biophysical interaction analyses, site-directed mutagenesis\",\n      \"journal\": \"Biophysical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction tests with mutagenesis and biophysical validation in a single lab\",\n      \"pmids\": [\"35331687\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PF3D7_0305700 was captured as an active E2 ubiquitin-conjugating enzyme by a ubiquitin activity-based probe (Ub-Dha) during P. falciparum asexual blood-stage development, and was validated through in vitro ubiquitination assays; it was also shown to have selective functional interactions with the HECT E3 ligase PfHEUL.\",\n      \"method\": \"Activity-based protein profiling (Ub-Dha probe), in vitro ubiquitination assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — activity-based probe capture plus in vitro assay validation, single lab, single study\",\n      \"pmids\": [\"40249735\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0305700 is an active E2 ubiquitin/SUMO-conjugating enzyme in P. falciparum that engages the SUMO E1-activating enzyme through species-specific surface residues (distinct from the human interface), interacts selectively with the HECT E3 ligase PfHEUL in ubiquitin transfer, and contributes to parasite survival under oxidative stress during asexual blood-stage development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0305700 is an active E2-conjugating enzyme of Plasmodium falciparum that operates in both the SUMO and ubiquitin conjugation systems during asexual blood-stage development [#0, #3]. In the SUMO pathway, it functions as the E2-conjugating enzyme that engages the P. falciparum SUMO E1-activating enzyme through surface residues distinct from the human E1–E2 interface [#0], and this SUMOylation activity contributes to protecting trophozoite-stage parasites against iron-induced oxidative stress [#1]. The parasite enzyme also displays species-specific SUMO recognition: whereas Pf-SUMO can engage human E2, Hs-SUMO1 fails to interact with PF3D7_0305700, a selectivity governed by critical N-terminal residues whose mutation to the human counterparts restores the cross-species interaction [#2]. In the ubiquitin pathway, PF3D7_0305700 was captured as a catalytically active E2 by a ubiquitin activity-based probe and validated in vitro, and it shows selective functional interaction with the HECT E3 ligase PfHEUL [#3]. Beyond these activities, the enzyme's full substrate repertoire and its in vivo genetic requirement remain uncharacterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Establishing how the parasite SUMO E2 engages its E1 partner was needed to define whether the conjugation interface diverges from the human system and could be selectively targeted; crystallography plus mutagenesis showed the P. falciparum E1–E2 interaction uses surface residues distinct from the human interface.\",\n      \"evidence\": \"X-ray crystallography of the human E1 ubiquitin fold domain–Ubc9 complex with in silico modeling, site-directed mutagenesis, and in vitro biochemistry of the P. falciparum enzymes\",\n      \"pmids\": [\"26697886\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal structure of the P. falciparum E1–E2 complex itself\", \"SUMO substrates conjugated via this E2 not identified\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"It was unclear whether SUMOylation had a defined physiological role in blood-stage parasites; oxidative-stress assays linked SUMOylation pathway activity, in which PF3D7_0305700 acts as the E2, to protection of trophozoites under iron-induced oxidative stress.\",\n      \"evidence\": \"Cell-based oxidative stress assays on asexual blood-stage P. falciparum\",\n      \"pmids\": [\"26697886\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Indirect readout without direct genetic perturbation of PF3D7_0305700\", \"Protective mechanism and relevant SUMOylated targets undefined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"To determine the structural basis of SUMO recognition specificity, cross-species interaction tests asked whether parasite and human components are interchangeable; they revealed a unidirectional interaction in which Hs-SUMO1 fails to engage PF3D7_0305700 owing to critical N-terminal residues, restorable by humanizing those residues.\",\n      \"evidence\": \"Biochemical and biophysical interaction analyses with site-directed mutagenesis and reciprocal cross-species interaction tests\",\n      \"pmids\": [\"35331687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Consequences of the specificity for in vivo SUMO conjugation not tested\", \"Single-lab biophysical characterization\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether PF3D7_0305700 also acts as a bona fide ubiquitin E2 in living parasites was open; activity-based probe capture during blood-stage growth plus in vitro ubiquitination confirmed it as an active ubiquitin-conjugating enzyme with selective interaction with the HECT E3 PfHEUL.\",\n      \"evidence\": \"Activity-based protein profiling with a Ub-Dha probe during P. falciparum asexual development and in vitro ubiquitination assays\",\n      \"pmids\": [\"40249735\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitination substrates and chain topology not defined\", \"Functional consequence of the PfHEUL interaction in vivo untested\", \"Single study, single lab\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether PF3D7_0305700 is genetically essential and what its physiological substrate set is across the SUMO and ubiquitin pathways in the intact parasite.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No conditional knockdown or knockout phenotype reported\", \"No in vivo substrate identification\", \"Relative contribution of SUMO versus ubiquitin conjugation roles undetermined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0061631\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0061656\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016925\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0016567\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0006979\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"P. falciparum SUMO E1-activating enzyme [#0]\",\n      \"Pf-SUMO [#2]\",\n      \"PfHEUL (HECT E3 ligase) [#3]\"\n    ],\n    \"other_free_text\": [\n      \"Engages the SUMO E1 via surface residues distinct from the human E1–E2 interface [#0].\",\n      \"Species-specific SUMO recognition governed by N-terminal residues; humanizing these restores Hs-SUMO1 interaction [#2].\",\n      \"Captured as an active E2 by a ubiquitin activity-based probe (Ub-Dha) during asexual blood-stage development [#3].\",\n      \"SUMOylation activity is protective under iron-induced oxidative stress in trophozoites [#1].\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0305700","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 3 of 3 cited papers name other catalogue genes (PF3D7_0505800, PF3D7_0915100, PF3D7_0811400). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0305700","name":null,"product":"ubiquitin-conjugating enzyme MMS2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0404200","name":null,"product":"ubiquitin-conjugating enzyme E2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0837000","name":null,"product":"ubiquitin-conjugating enzyme MMS2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}