{"gene":"PF3D7_1433400","run_date":"2026-09-08T14:19:07","timeline":{"discoveries":[{"year":2021,"finding":"PHD2 (PF3D7_1433400) was identified as a subunit of the divergent PfGCN5 histone acetyltransferase complex in P. falciparum, which also contains PfPHD1 and an AP2-domain transcription factor (PfAP2-LT). The complex was shown to be required for erythrocyte invasion and var gene regulation, though the specific functional contribution of PHD2 itself (as distinct from the complex or PfPHD1) was not separately delineated in these experiments.","method":"Co-immunoprecipitation / complex identification; domain deletion mutagenesis of sibling subunit PfPHD1 and PfGCN5 bromodomain (not PHD2 itself)","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — PHD2 membership in the complex was established by co-IP/complex identification in a single lab study; functional experiments were performed on sibling subunits, not PHD2 directly","pmids":["34403450"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PHD2 (PF3D7_1433400) is a subunit of the divergent PfGCN5 histone acetyltransferase (SAGA-like) complex in P. falciparum, alongside PfPHD1 and the AP2-domain factor PfAP2-LT; beyond its membership in this complex, no direct mechanistic function has been experimentally established for PHD2 itself in the available literature."},"narrative":{"mechanistic_narrative":"PHD2 (PF3D7_1433400) is a PHD finger protein identified as a subunit of the divergent PfGCN5 histone acetyltransferase (SAGA-like) complex in Plasmodium falciparum, which also contains the sibling subunit PfPHD1 and the AP2-domain transcription factor PfAP2-LT [PMID:34403450]. This complex is required for erythrocyte invasion and var gene regulation, but the functional experiments that established these roles were performed on the sibling subunits PfPHD1 and the PfGCN5 bromodomain rather than on PHD2 itself, so the specific mechanistic contribution of PHD2 has not been separately delineated [PMID:34403450]. Beyond its membership in this complex [PMID:34403450], no direct function, substrate, or chromatin target has been experimentally established for PHD2 in the available corpus.","teleology":[{"year":2021,"claim":"Establishing the composition of the divergent PfGCN5 acetyltransferase complex placed PHD2 within a defined chromatin-modifying machinery, answering whether this PHD finger protein participates in a larger regulatory assembly.","evidence":"Co-immunoprecipitation and complex identification in P. falciparum, with domain-deletion mutagenesis of the sibling subunits PfPHD1 and the PfGCN5 bromodomain","pmids":["34403450"],"confidence":"Medium","gaps":["The functional contribution of PHD2 itself was not tested; deletion/mutagenesis targeted sibling subunits, not PHD2","No substrate, histone mark, or chromatin-binding specificity has been assigned to PHD2's PHD finger","Whether PHD2 is required for erythrocyte invasion or var gene regulation independent of the intact complex is unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct molecular activity of PHD2 within the PfGCN5 complex remains undefined, including whether its PHD finger reads a specific histone modification and what phenotype loss of PHD2 alone produces.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No PHD2-specific genetic perturbation reported","No structural or biochemical characterization of the PHD2 PHD finger","No demonstration of an independent role separable from the complex or from PfPHD1"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Divergent PfGCN5 histone acetyltransferase (SAGA-like) complex (with PfPHD1 and PfAP2-LT) [#0]"],"partners":["PFPHD1 [#0]","PFGCN5 [#0]","PFAP2-LT [#0]"],"other_free_text":["PHD2 (PF3D7_1433400) membership in the PfGCN5 complex is established, but no direct mechanistic function has been experimentally assigned to PHD2 itself; complex-level roles in erythrocyte invasion and var gene regulation were demonstrated through sibling subunits, not PHD2 [#0]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"34403450","id":"PMC_34403450","title":"A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34403450","citation_count":44,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PHD","PfPHD2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34418264","id":"PMC_34418264","title":"Zinc finger proteins of Plasmodium falciparum.","date":"2021","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34418264","citation_count":33,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PHD"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34389510","id":"PMC_34389510","title":"Plasmodium falciparum SET2 domain is allosterically regulated by its PHD-like domain to methylate at H3K36.","date":"2021","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/34389510","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PHD"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4425,"output_tokens":469,"usd":0.010155,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4958,"output_tokens":1249,"usd":0.028008,"stage2_stop_reason":"end_turn"},"total_usd":0.038163,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"PHD2 (PF3D7_1433400) was identified as a subunit of the divergent PfGCN5 histone acetyltransferase complex in P. falciparum, which also contains PfPHD1 and an AP2-domain transcription factor (PfAP2-LT). The complex was shown to be required for erythrocyte invasion and var gene regulation, though the specific functional contribution of PHD2 itself (as distinct from the complex or PfPHD1) was not separately delineated in these experiments.\",\n      \"method\": \"Co-immunoprecipitation / complex identification; domain deletion mutagenesis of sibling subunit PfPHD1 and PfGCN5 bromodomain (not PHD2 itself)\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — PHD2 membership in the complex was established by co-IP/complex identification in a single lab study; functional experiments were performed on sibling subunits, not PHD2 directly\",\n      \"pmids\": [\"34403450\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PHD2 (PF3D7_1433400) is a subunit of the divergent PfGCN5 histone acetyltransferase (SAGA-like) complex in P. falciparum, alongside PfPHD1 and the AP2-domain factor PfAP2-LT; beyond its membership in this complex, no direct mechanistic function has been experimentally established for PHD2 itself in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PHD2 (PF3D7_1433400) is a PHD finger protein identified as a subunit of the divergent PfGCN5 histone acetyltransferase (SAGA-like) complex in Plasmodium falciparum, which also contains the sibling subunit PfPHD1 and the AP2-domain transcription factor PfAP2-LT [#0]. This complex is required for erythrocyte invasion and var gene regulation, but the functional experiments that established these roles were performed on the sibling subunits PfPHD1 and the PfGCN5 bromodomain rather than on PHD2 itself, so the specific mechanistic contribution of PHD2 has not been separately delineated [#0]. Beyond its membership in this complex [#0], no direct function, substrate, or chromatin target has been experimentally established for PHD2 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"Establishing the composition of the divergent PfGCN5 acetyltransferase complex placed PHD2 within a defined chromatin-modifying machinery, answering whether this PHD finger protein participates in a larger regulatory assembly.\",\n      \"evidence\": \"Co-immunoprecipitation and complex identification in P. falciparum, with domain-deletion mutagenesis of the sibling subunits PfPHD1 and the PfGCN5 bromodomain\",\n      \"pmids\": [\n        \"34403450\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The functional contribution of PHD2 itself was not tested; deletion/mutagenesis targeted sibling subunits, not PHD2\",\n        \"No substrate, histone mark, or chromatin-binding specificity has been assigned to PHD2's PHD finger\",\n        \"Whether PHD2 is required for erythrocyte invasion or var gene regulation independent of the intact complex is unknown\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular activity of PHD2 within the PfGCN5 complex remains undefined, including whether its PHD finger reads a specific histone modification and what phenotype loss of PHD2 alone produces.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No PHD2-specific genetic perturbation reported\",\n        \"No structural or biochemical characterization of the PHD2 PHD finger\",\n        \"No demonstration of an independent role separable from the complex or from PfPHD1\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\n      \"Divergent PfGCN5 histone acetyltransferase (SAGA-like) complex (with PfPHD1 and PfAP2-LT) [#0]\"\n    ],\n    \"partners\": [\n      \"PfPHD1 [#0]\",\n      \"PfGCN5 [#0]\",\n      \"PfAP2-LT [#0]\"\n    ],\n    \"other_free_text\": [\n      \"PHD2 (PF3D7_1433400) membership in the PfGCN5 complex is established, but no direct mechanistic function has been experimentally assigned to PHD2 itself; complex-level roles in erythrocyte invasion and var gene regulation were demonstrated through sibling subunits, not PHD2 [#0].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1433400","name":null,"product":"PHD finger protein PHD2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1011500","name":null,"product":"PHD finger protein PHD2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0420000","name":null,"product":"PHD finger protein PHD2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"PHD2","evaluation":null}