{"gene":"PF3D7_0303900","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":1995,"finding":"PF3D7_0303900 was identified as a putative phosphatidylethanolamine-binding protein (PEBP) in P. falciparum by determination of its primary amino acid sequence, establishing it as a member of the PEBP sequence family.","method":"Molecular cloning and primary structure determination","journal":"Molecular and biochemical parasitology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — sequence-based identification only, no biochemical functional validation reported in abstract","pmids":["7637711"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"The crystal structure of the P. vivax ortholog of PF3D7_0303900 (a putative RKIP/PEBP homolog) was solved to 1.3 Å resolution by multi-wavelength anomalous diffraction; the structure is topologically similar to other PEBP family members but contains a distinctive left-handed alpha-helical region at one side of the canonical phospholipid-binding site, suggesting it represents a structurally distinct subfamily of the PEBP family.","method":"X-ray crystallography (MAD phasing, 1.3 Å resolution)","journal":"Acta crystallographica. Section F, Structural biology and crystallization communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution crystal structure in orthologous P. vivax protein, single study, no functional mutagenesis reported","pmids":["17329808"],"is_preprint":false,"attribution":[{"species":"Plasmodium vivax","strain":""}]},{"year":2025,"finding":"PfRKIP (PF3D7_0303900) is expressed throughout asexual schizogony with maximum expression in late schizonts, and at physiological pH binds phosphatidic acid and phosphorylated phosphatidylinositol lipids (e.g., PtdIns(3)P); this lipid binding is mediated by a unique IKK motif and conserved residues in the PEBP domain, as shown by mutagenesis that reduced PtdIns(3)P interaction.","method":"Lipid-binding assays (pH-dependent), PEBP domain mutagenesis, in silico docking","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (lipid binding assay, mutagenesis, docking) in a single lab study establishing lipid-binding specificity","pmids":["39842334"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PfRKIP (PF3D7_0303900) physically interacts with the essential kinase PfCDPK1 within P. falciparum parasites, as demonstrated by ELISA, immunofluorescence assay co-localization, and proximity biotinylation; PfRKIP inhibits PfCDPK1 kinase activity, and in the presence of PfCDPK1 substrate, PfCDPK1 hyper-phosphorylates PfRKIP, causing dissociation of the complex and allowing PfCDPK1 to trans-phosphorylate its downstream substrates.","method":"ELISA (protein-protein interaction), immunofluorescence assay, proximity biotinylation (BioID), kinase activity assay, phosphorylation/dissociation assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal in-cell and biochemical methods (proximity biotinylation, IFA, ELISA, kinase assay) in a single lab establishing interaction and regulatory mechanism","pmids":["39842334"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0303900 (PfRKIP) is a phosphatidylethanolamine-binding protein family member expressed in P. falciparum asexual stages (peak in late schizonts) that binds phosphatidic acid and phosphorylated phosphatidylinositols via conserved PEBP-domain residues and a unique IKK motif; it physically interacts with the essential kinase PfCDPK1 to inhibit its activity, and is hyper-phosphorylated by PfCDPK1 upon substrate engagement, triggering complex dissociation and enabling PfCDPK1-mediated trans-phosphorylation of downstream targets."},"narrative":{"mechanistic_narrative":"PF3D7_0303900 (PfRKIP) is a phosphatidylethanolamine-binding protein (PEBP) family member of P. falciparum that functions as a lipid-responsive regulator of the essential kinase PfCDPK1 during asexual blood-stage schizogony [PMID:7637711, PMID:39842334]. It is expressed throughout schizogony with peak abundance in late schizonts, and at physiological pH binds phosphatidic acid and phosphorylated phosphatidylinositol lipids such as PtdIns(3)P through a distinctive IKK motif and conserved PEBP-domain residues, as defined by mutagenesis that reduced PtdIns(3)P interaction [PMID:39842334]. PfRKIP physically associates with PfCDPK1 in the parasite and inhibits its kinase activity; upon substrate engagement, PfCDPK1 hyper-phosphorylates PfRKIP, driving dissociation of the complex and permitting PfCDPK1 to trans-phosphorylate its downstream targets [PMID:39842334]. The high-resolution crystal structure of the P. vivax ortholog shows the canonical PEBP fold augmented by a distinctive left-handed alpha-helical region beside the phospholipid-binding site, marking this protein as a structurally distinct PEBP subfamily [PMID:17329808]. Beyond this lipid-binding and kinase-regulatory role, no further mechanistic detail for PF3D7_0303900 has been characterized in the available corpus.","teleology":[{"year":1995,"claim":"Establishing the identity of an uncharacterized Plasmodium protein was the first step; sequencing placed PF3D7_0303900 in the PEBP family, framing all later functional hypotheses.","evidence":"Molecular cloning and primary amino acid sequence determination in P. falciparum","pmids":["7637711"],"confidence":"Low","gaps":["Sequence-based classification only, with no biochemical or functional validation","No lipid-binding, structural, or partner information at this stage"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"Whether the PEBP assignment corresponded to a genuine fold, and whether the Plasmodium protein differed structurally from canonical PEBPs, was resolved by solving the ortholog structure.","evidence":"X-ray crystallography (MAD phasing, 1.3 Å) of the P. vivax ortholog","pmids":["17329808"],"confidence":"Medium","gaps":["Structure determined in the P. vivax ortholog, not PF3D7_0303900 itself","No functional mutagenesis mapping the significance of the distinctive alpha-helical region","Structure alone did not identify ligands or binding partners"],"attribution":[{"species":"Plasmodium vivax","strain":""}]},{"year":2025,"claim":"The specific lipid ligand of the protein and the residues responsible were unknown; binding assays and mutagenesis defined phosphatidic acid and phosphoinositide recognition via the IKK motif and PEBP-domain residues, giving the protein a defined biochemical activity.","evidence":"pH-dependent lipid-binding assays, PEBP-domain mutagenesis, and in silico docking in P. falciparum","pmids":["39842334"],"confidence":"Medium","gaps":["Single-lab study without independent replication","Physiological consequence of lipid binding within the parasite not established","Whether lipid binding modulates the PfCDPK1 interaction was not directly tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"How this PEBP protein connects to parasite signaling was addressed by showing it binds and inhibits the essential kinase PfCDPK1, establishing a substrate-triggered phospho-switch regulatory role.","evidence":"ELISA, immunofluorescence co-localization, proximity biotinylation (BioID), kinase activity and phosphorylation/dissociation assays in P. falciparum","pmids":["39842334"],"confidence":"Medium","gaps":["Single-lab study; interaction not confirmed by an independent group","Downstream PfCDPK1 substrates whose trans-phosphorylation is gated by PfRKIP were not identified","No genetic knockout/knockdown phenotype establishing the requirement of PfRKIP for parasite growth"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether lipid binding and PfCDPK1 regulation are mechanistically coupled and what biological process this controls in the parasite.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genetic loss-of-function phenotype for PF3D7_0303900 reported","Link between phosphoinositide/phosphatidic acid binding and PfCDPK1 inhibition not experimentally connected","Cellular process (e.g. egress/invasion) regulated by the PfRKIP–PfCDPK1 switch not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfRKIP–PfCDPK1 complex"],"partners":["PFCDPK1"],"other_free_text":["Expressed throughout asexual schizogony with peak expression in late schizonts [#2]","Binds phosphatidic acid and phosphorylated phosphatidylinositols (e.g. PtdIns(3)P) via a unique IKK motif and conserved PEBP-domain residues [#2]","P. vivax ortholog crystal structure shows canonical PEBP fold plus a distinctive left-handed alpha-helical region beside the phospholipid-binding site [#1]","Substrate-triggered phospho-switch: PfCDPK1 hyper-phosphorylation of PfRKIP dissociates the inhibitory complex and enables PfCDPK1 trans-phosphorylation of downstream targets [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"7637711","id":"PMC_7637711","title":"The primary structure of a putative phosphatidylethanolamine-binding protein from Plasmodium falciparum.","date":"1995","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/7637711","citation_count":19,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["phosphatidylethanolamine-binding protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17329808","id":"PMC_17329808","title":"The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix.","date":"2007","source":"Acta crystallographica. Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/17329808","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["phosphatidylethanolamine-binding protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39842334","id":"PMC_39842334","title":"Plasmodium falciparum raf kinase inhibitor is a lipid binding protein that interacts with and regulates the activity of PfCDPK1, an essential plant-like kinase required for red blood cell invasion.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/39842334","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["phosphatidylethanolamine-binding protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3937,"output_tokens":1331,"usd":0.015888,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6142,"output_tokens":2665,"usd":0.048668,"stage2_stop_reason":"end_turn"},"total_usd":0.064556,"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\": 1995,\n      \"finding\": \"PF3D7_0303900 was identified as a putative phosphatidylethanolamine-binding protein (PEBP) in P. falciparum by determination of its primary amino acid sequence, establishing it as a member of the PEBP sequence family.\",\n      \"method\": \"Molecular cloning and primary structure determination\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — sequence-based identification only, no biochemical functional validation reported in abstract\",\n      \"pmids\": [\"7637711\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The crystal structure of the P. vivax ortholog of PF3D7_0303900 (a putative RKIP/PEBP homolog) was solved to 1.3 Å resolution by multi-wavelength anomalous diffraction; the structure is topologically similar to other PEBP family members but contains a distinctive left-handed alpha-helical region at one side of the canonical phospholipid-binding site, suggesting it represents a structurally distinct subfamily of the PEBP family.\",\n      \"method\": \"X-ray crystallography (MAD phasing, 1.3 Å resolution)\",\n      \"journal\": \"Acta crystallographica. Section F, Structural biology and crystallization communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution crystal structure in orthologous P. vivax protein, single study, no functional mutagenesis reported\",\n      \"pmids\": [\"17329808\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium vivax\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfRKIP (PF3D7_0303900) is expressed throughout asexual schizogony with maximum expression in late schizonts, and at physiological pH binds phosphatidic acid and phosphorylated phosphatidylinositol lipids (e.g., PtdIns(3)P); this lipid binding is mediated by a unique IKK motif and conserved residues in the PEBP domain, as shown by mutagenesis that reduced PtdIns(3)P interaction.\",\n      \"method\": \"Lipid-binding assays (pH-dependent), PEBP domain mutagenesis, in silico docking\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (lipid binding assay, mutagenesis, docking) in a single lab study establishing lipid-binding specificity\",\n      \"pmids\": [\"39842334\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfRKIP (PF3D7_0303900) physically interacts with the essential kinase PfCDPK1 within P. falciparum parasites, as demonstrated by ELISA, immunofluorescence assay co-localization, and proximity biotinylation; PfRKIP inhibits PfCDPK1 kinase activity, and in the presence of PfCDPK1 substrate, PfCDPK1 hyper-phosphorylates PfRKIP, causing dissociation of the complex and allowing PfCDPK1 to trans-phosphorylate its downstream substrates.\",\n      \"method\": \"ELISA (protein-protein interaction), immunofluorescence assay, proximity biotinylation (BioID), kinase activity assay, phosphorylation/dissociation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal in-cell and biochemical methods (proximity biotinylation, IFA, ELISA, kinase assay) in a single lab establishing interaction and regulatory mechanism\",\n      \"pmids\": [\"39842334\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0303900 (PfRKIP) is a phosphatidylethanolamine-binding protein family member expressed in P. falciparum asexual stages (peak in late schizonts) that binds phosphatidic acid and phosphorylated phosphatidylinositols via conserved PEBP-domain residues and a unique IKK motif; it physically interacts with the essential kinase PfCDPK1 to inhibit its activity, and is hyper-phosphorylated by PfCDPK1 upon substrate engagement, triggering complex dissociation and enabling PfCDPK1-mediated trans-phosphorylation of downstream targets.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0303900 (PfRKIP) is a phosphatidylethanolamine-binding protein (PEBP) family member of P. falciparum that functions as a lipid-responsive regulator of the essential kinase PfCDPK1 during asexual blood-stage schizogony [#0, #3]. It is expressed throughout schizogony with peak abundance in late schizonts, and at physiological pH binds phosphatidic acid and phosphorylated phosphatidylinositol lipids such as PtdIns(3)P through a distinctive IKK motif and conserved PEBP-domain residues, as defined by mutagenesis that reduced PtdIns(3)P interaction [#2]. PfRKIP physically associates with PfCDPK1 in the parasite and inhibits its kinase activity; upon substrate engagement, PfCDPK1 hyper-phosphorylates PfRKIP, driving dissociation of the complex and permitting PfCDPK1 to trans-phosphorylate its downstream targets [#3]. The high-resolution crystal structure of the P. vivax ortholog shows the canonical PEBP fold augmented by a distinctive left-handed alpha-helical region beside the phospholipid-binding site, marking this protein as a structurally distinct PEBP subfamily [#1]. Beyond this lipid-binding and kinase-regulatory role, no further mechanistic detail for PF3D7_0303900 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Establishing the identity of an uncharacterized Plasmodium protein was the first step; sequencing placed PF3D7_0303900 in the PEBP family, framing all later functional hypotheses.\",\n      \"evidence\": \"Molecular cloning and primary amino acid sequence determination in P. falciparum\",\n      \"pmids\": [\n        \"7637711\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Sequence-based classification only, with no biochemical or functional validation\",\n        \"No lipid-binding, structural, or partner information at this stage\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Whether the PEBP assignment corresponded to a genuine fold, and whether the Plasmodium protein differed structurally from canonical PEBPs, was resolved by solving the ortholog structure.\",\n      \"evidence\": \"X-ray crystallography (MAD phasing, 1.3 Å) of the P. vivax ortholog\",\n      \"pmids\": [\n        \"17329808\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structure determined in the P. vivax ortholog, not PF3D7_0303900 itself\",\n        \"No functional mutagenesis mapping the significance of the distinctive alpha-helical region\",\n        \"Structure alone did not identify ligands or binding partners\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium vivax\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The specific lipid ligand of the protein and the residues responsible were unknown; binding assays and mutagenesis defined phosphatidic acid and phosphoinositide recognition via the IKK motif and PEBP-domain residues, giving the protein a defined biochemical activity.\",\n      \"evidence\": \"pH-dependent lipid-binding assays, PEBP-domain mutagenesis, and in silico docking in P. falciparum\",\n      \"pmids\": [\n        \"39842334\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab study without independent replication\",\n        \"Physiological consequence of lipid binding within the parasite not established\",\n        \"Whether lipid binding modulates the PfCDPK1 interaction was not directly tested\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"How this PEBP protein connects to parasite signaling was addressed by showing it binds and inhibits the essential kinase PfCDPK1, establishing a substrate-triggered phospho-switch regulatory role.\",\n      \"evidence\": \"ELISA, immunofluorescence co-localization, proximity biotinylation (BioID), kinase activity and phosphorylation/dissociation assays in P. falciparum\",\n      \"pmids\": [\n        \"39842334\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab study; interaction not confirmed by an independent group\",\n        \"Downstream PfCDPK1 substrates whose trans-phosphorylation is gated by PfRKIP were not identified\",\n        \"No genetic knockout/knockdown phenotype establishing the requirement of PfRKIP for parasite growth\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether lipid binding and PfCDPK1 regulation are mechanistically coupled and what biological process this controls in the parasite.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic loss-of-function phenotype for PF3D7_0303900 reported\",\n        \"Link between phosphoinositide/phosphatidic acid binding and PfCDPK1 inhibition not experimentally connected\",\n        \"Cellular process (e.g. egress/invasion) regulated by the PfRKIP–PfCDPK1 switch not defined\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0008429\",\n        \"supporting_discovery_ids\": [\n          0,\n          2\n        ]\n      },\n      {\n        \"term_id\": \"GO:0005543\",\n        \"supporting_discovery_ids\": [\n          2\n        ]\n      },\n      {\n        \"term_id\": \"GO:0043495\",\n        \"supporting_discovery_ids\": [\n          2\n        ]\n      },\n      {\n        \"term_id\": \"GO:0019210\",\n        \"supporting_discovery_ids\": [\n          3\n        ]\n      },\n      {\n        \"term_id\": \"GO:0019901\",\n        \"supporting_discovery_ids\": [\n          3\n        ]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0035556\",\n        \"supporting_discovery_ids\": [\n          3\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"PfRKIP–PfCDPK1 complex\"\n    ],\n    \"partners\": [\n      \"PfCDPK1\"\n    ],\n    \"other_free_text\": [\n      \"Expressed throughout asexual schizogony with peak expression in late schizonts [#2]\",\n      \"Binds phosphatidic acid and phosphorylated phosphatidylinositols (e.g. PtdIns(3)P) via a unique IKK motif and conserved PEBP-domain residues [#2]\",\n      \"P. vivax ortholog crystal structure shows canonical PEBP fold plus a distinctive left-handed alpha-helical region beside the phospholipid-binding site [#1]\",\n      \"Substrate-triggered phospho-switch: PfCDPK1 hyper-phosphorylation of PfRKIP dissociates the inhibitory complex and enables PfCDPK1 trans-phosphorylation of downstream targets [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0303900","name":null,"product":"phosphatidylethanolamine-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0402500","name":null,"product":"phosphatidylethanolamine-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0839200","name":null,"product":"phosphatidylethanolamine-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}