{"gene":"PF3D7_0213400","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2005,"finding":"Recombinant PK7 (PfPK7) displays kinase activity toward a variety of substrates in vitro but is unable to phosphorylate the two P. falciparum MAPK homologues (PfMAP1 and PfMAP2), and is insensitive to PKA and MEK inhibitors. PK7 lacks a typical MAPKK activation site in its T-loop, distinguishing it from canonical MAPKKs despite highest sequence similarity to the MAPKK3/6 subgroup in its C-terminal lobe and similarity to fungal PKA in its N-terminal region.","method":"Recombinant protein expression and in vitro kinase assay; inhibitor profiling; blastp sequence analysis","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro kinase assay with defined substrates and mutagenesis-equivalent negative controls (inability to phosphorylate MAPKs, inhibitor insensitivity), single lab but multiple orthogonal methods","pmids":["15612927"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"Genetic disruption of PK7 (pfpk7-) causes two distinct phenotypes: (1) reduced asexual growth rate in erythrocytes with fewer daughter merozoites per schizont, and (2) dramatic reduction in oocyst production in the mosquito vector. Both phenotypes are rescued by reintroduction of a functional pfpk7 gene, establishing PK7 as necessary for parasite proliferation during schizogony and for sporogony.","method":"Reverse genetics (gene disruption); phenotypic analysis of asexual growth and oocyst counts; genetic complementation","journal":"Eukaryotic cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined cellular phenotypes at two life-cycle stages, confirmed by genetic complementation, single lab with rigorous controls","pmids":["18083830"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"Crystal structure of PK7 reveals that the enzyme adopts a constitutively active conformation stabilized by an arginine residue in the activation loop that substitutes for the conserved phosphorylated residue that structures the activation loop in canonical kinases. The structure also reveals how extensive insertions are accommodated as excursions from the canonical eukaryotic protein kinase fold.","method":"X-ray crystallography; structural analysis of activation loop conformation","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional interpretation of activation mechanism; single lab but high-quality structural data with mechanistic consequence","pmids":["18275814"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"PK7 is required for melatonin signal transduction in P. falciparum: in pfpk7- parasites, melatonin treatment fails to (i) alter the ratio of asexual stages, (ii) induce a rise in cytoplasmic calcium, and (iii) up-regulate ubiquitin/proteasome system (UPS) gene transcription. Wild-type responses to melatonin are restored by complementation with a functional pfpk7 gene, placing PK7 upstream of calcium signaling and UPS gene regulation in the melatonin pathway.","method":"Gene knockout (pfpk7-) and genetic complementation; real-time PCR of UPS genes; calcium measurement; cell-cycle stage ratio analysis","journal":"Journal of pineal research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — KO with multiple orthogonal readouts (calcium, transcription, cell-cycle staging) and genetic rescue, single lab","pmids":["22348509"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"Loss of PK7 in pfpk7- parasites causes major alterations in the expression of mitochondrial fission genes (FIS1, DYN1, DYN2) and abolishes melatonin-induced changes in fission protein expression. Mitochondrial functional characteristics (oxygen consumption) are profoundly altered in pfpk7- parasites, indicating PK7 plays a role in control of mitochondrial morphogenesis and maturation during intra-erythrocyte cell cycle progression.","method":"Gene knockout (pfpk7-); qRT-PCR of fission genes; MitoTracker staining; oxygen consumption measurement; GFP-mitochondrial matrix reporter","journal":"Journal of pineal research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — KO with multiple phenotypic readouts (transcription, morphology, respiration) but no direct biochemical link between PK7 and fission machinery; single lab","pmids":["29480948"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"Comparative quantitative phosphoproteomics of wild-type vs. pfpk7- parasites at schizont and segmenter stages identified 146 proteins with 239 phosphorylation sites showing reduced phosphorylation in the absence of PK7, and three phosphorylation motifs down-regulated in both stages. Direct in vitro kinase assays confirmed PK7 phosphorylates three of these candidate substrates, while many others showed indirect reduction in phosphorylation, revealing both direct substrates and downstream/compensatory signaling effects.","method":"Isobaric tag-based quantitative phosphoproteomics (TMT); in vitro kinase assay with candidate substrates; gene knockout (pfpk7-)","journal":"Journal of proteome research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — phosphoproteomics combined with direct in vitro kinase assay validation of substrates, multiple orthogonal methods in one study, single lab","pmids":["29678115"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"PfMORC expression is severely affected in pfpk7- parasites following melatonin treatment, placing PK7 upstream of PfMORC in the melatonin signaling pathway that regulates asexual stage synchronization.","method":"Gene knockout (pfpk7-); real-time expression assay of PfMORC; melatonin treatment","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — epistasis inferred from KO transcriptional readout, single lab, no direct biochemical interaction shown between PK7 and PfMORC","pmids":["33479315"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]}],"current_model":"PK7 (PF3D7_0213400) is an atypical, constitutively active orphan kinase whose activation loop arginine substitutes for the canonical phosphorylated residue; it phosphorylates diverse substrates (identified by phosphoproteomics and direct in vitro assay) but not the P. falciparum MAPK homologues, and functions upstream of calcium signaling, ubiquitin/proteasome gene regulation, and PfMORC expression in the melatonin transduction pathway, while also being required for schizont-stage merozoite production and mosquito-stage oocyst development."},"narrative":{"mechanistic_narrative":"PK7 (PF3D7_0213400) is an atypical orphan protein kinase of P. falciparum that governs parasite proliferation and melatonin signal transduction across the life cycle [PMID:18083830, PMID:22348509]. It is a constitutively active enzyme: its crystal structure shows an arginine residue in the activation loop substituting for the conserved phosphorylated residue that normally structures this region in canonical kinases, and it accommodates large insertions as excursions from the eukaryotic protein kinase fold [PMID:18275814]. Recombinant PK7 phosphorylates diverse substrates in vitro but does not phosphorylate the P. falciparum MAPK homologues PfMAP1 and PfMAP2 and is insensitive to PKA and MEK inhibitors, distinguishing it from a canonical MAPKK despite C-terminal similarity to the MAPKK3/6 subgroup and N-terminal similarity to fungal PKA [PMID:15612927]. Quantitative phosphoproteomics of pfpk7-null parasites identified 146 proteins with reduced phosphorylation and confirmed three of these as direct in vitro substrates, defining both direct targets and downstream signaling effects [PMID:29678115]. Genetically, PK7 is required for schizogony, producing fewer daughter merozoites per schizont when disrupted, and for mosquito-stage oocyst formation, with both phenotypes rescued by complementation [PMID:18083830]. Functionally, PK7 acts upstream in the melatonin transduction pathway, being necessary for melatonin-induced cytoplasmic calcium rise, up-regulation of ubiquitin/proteasome system genes, and PfMORC expression, and it also influences expression of mitochondrial fission genes and mitochondrial respiration during intra-erythrocytic development [PMID:22348509, PMID:29480948, PMID:33479315]. No direct biochemical link between PK7 and the mitochondrial fission machinery or PfMORC has been established in the available corpus.","teleology":[{"year":2005,"claim":"Whether PK7, annotated by sequence as MAPKK-like, actually functions as a MAP kinase kinase was unknown; the biochemistry showed it is an active kinase but not a functional MAPKK.","evidence":"Recombinant kinase assay with defined substrates, inhibitor profiling, and blastp analysis in P. falciparum","pmids":["15612927"],"confidence":"High","gaps":["Physiological substrates not identified","Lacks canonical MAPKK activation site — activation mechanism unexplained at this stage"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"The cellular requirement for PK7 was unknown; gene disruption established that it is needed for asexual schizogony and for mosquito-stage sporogony.","evidence":"Reverse-genetic knockout with phenotyping and genetic complementation in P. falciparum","pmids":["18083830"],"confidence":"High","gaps":["Molecular pathway linking PK7 to merozoite number and oocyst formation not defined","Substrates driving these phenotypes unidentified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"The activation state of an orphan kinase lacking a canonical T-loop phosphosite was unclear; the structure revealed a constitutively active conformation stabilized by an activation-loop arginine.","evidence":"X-ray crystallography and structural analysis of activation-loop conformation in P. falciparum PK7","pmids":["18275814"],"confidence":"High","gaps":["No substrate-bound or inhibitor-bound structures","Regulation of an already-active kinase in vivo unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"Where PK7 sits in a signaling pathway was unknown; knockout placed it upstream of melatonin-induced calcium signaling and ubiquitin/proteasome gene regulation.","evidence":"pfpk7- knockout and complementation with calcium measurement, UPS gene qPCR, and cell-cycle staging in P. falciparum","pmids":["22348509"],"confidence":"High","gaps":["Direct substrates transmitting the melatonin signal not identified","Mechanism coupling PK7 to calcium mobilization unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"Whether PK7 influences organellar biogenesis was unknown; knockout showed altered mitochondrial fission gene expression and respiration during the intra-erythrocytic cycle.","evidence":"pfpk7- knockout with fission-gene qRT-PCR, MitoTracker/GFP reporter imaging, and oxygen consumption in P. falciparum","pmids":["29480948"],"confidence":"Medium","gaps":["No direct biochemical link between PK7 and fission machinery (FIS1, DYN1, DYN2)","Effects may be indirect downstream consequences of the growth defect"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"The direct substrates of PK7 were undefined; comparative phosphoproteomics of null parasites mapped PK7-dependent phosphosites and validated three direct substrates in vitro.","evidence":"TMT quantitative phosphoproteomics of wild-type vs pfpk7- schizonts/segmenters plus in vitro kinase assays in P. falciparum","pmids":["29678115"],"confidence":"High","gaps":["Most of the 146 affected proteins are indirect and their upstream kinases unresolved","Identity/function of the three validated substrates not developmentally contextualized"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"Whether PK7 controls downstream chromatin/transcriptional regulators in the melatonin pathway was unknown; knockout showed PfMORC expression is impaired after melatonin treatment.","evidence":"pfpk7- knockout with real-time PfMORC expression assay following melatonin treatment in P. falciparum 3D7","pmids":["33479315"],"confidence":"Medium","gaps":["Epistasis inferred from transcription only — no direct PK7–PfMORC biochemical interaction","Intermediate steps between PK7 and PfMORC regulation unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":null,"claim":"The physiological substrate(s) that mechanistically link PK7 to calcium mobilization, UPS/PfMORC gene regulation, merozoite production, and oocyst development remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No substrate mapped to a specific downstream phenotype","No interaction partner or scaffold identified","How a constitutively active kinase is signal-regulated by melatonin is unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["Constitutively active orphan kinase; activation-loop arginine substitutes for the canonical phosphorylated activation residue [#2]","Does not phosphorylate P. falciparum MAPK homologues PfMAP1/PfMAP2 and is insensitive to PKA and MEK inhibitors [#0]","Required for schizont-stage merozoite production and mosquito-stage oocyst development [#1]","Acts upstream of melatonin-induced calcium rise, UPS gene transcription, and PfMORC expression [#3, #6]","Influences mitochondrial fission gene expression and respiration during intra-erythrocytic development [#4]","Three direct in vitro substrates validated from phosphoproteomics of pfpk7- parasites [#5]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"15612927","id":"PMC_15612927","title":"PfPK7, an atypical MEK-related protein kinase, reflects the absence of classical three-component MAPK pathways in the human malaria parasite Plasmodium falciparum.","date":"2005","source":"Molecular 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1993)","url":"https://pubmed.ncbi.nlm.nih.gov/18275814","citation_count":56,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["protein kinase 7","PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16513357","id":"PMC_16513357","title":"Antimalarial potential of xestoquinone, a protein kinase inhibitor isolated from a Vanuatu marine sponge Xestospongia sp.","date":"2006","source":"Bioorganic & medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16513357","citation_count":49,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26934697","id":"PMC_26934697","title":"Biochemical Screening of Five Protein Kinases from Plasmodium falciparum against 14,000 Cell-Active Compounds.","date":"2016","source":"PloS 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falciparum.","date":"2012","source":"Journal of pineal research","url":"https://pubmed.ncbi.nlm.nih.gov/22348509","citation_count":33,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19675896","id":"PMC_19675896","title":"Synthesis of 3-(1,2,3-triazol-1-yl)- and 3-(1,2,3-triazol-4-yl)-substituted pyrazolo[3,4-d]pyrimidin-4-amines via click chemistry: potential inhibitors of the Plasmodium falciparum PfPK7 protein kinase.","date":"2009","source":"Organic & biomolecular chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19675896","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18774709","id":"PMC_18774709","title":"Synthesis and in vitro evaluation of imidazopyridazines as novel inhibitors of the malarial kinase PfPK7.","date":"2008","source":"Bioorganic & medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/18774709","citation_count":28,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29678115","id":"PMC_29678115","title":"Characterization of Plasmodium falciparum Atypical Kinase PfPK7- Dependent Phosphoproteome.","date":"2018","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/29678115","citation_count":22,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28050233","id":"PMC_28050233","title":"Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP.","date":"2016","source":"Genes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/28050233","citation_count":18,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["protein kinase 7","PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25479077","id":"PMC_25479077","title":"Melatonin-induced temporal up-regulation of gene expression related to ubiquitin/proteasome system (UPS) in the human malaria parasite Plasmodium falciparum.","date":"2014","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/25479077","citation_count":16,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["protein kinase 7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"33479315","id":"PMC_33479315","title":"A nuclear protein, PfMORC confers melatonin dependent synchrony of the human malaria parasite P. falciparum in the asexual stage.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33479315","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32867164","id":"PMC_32867164","title":"Role of Melatonin in the Synchronization of Asexual Forms in the Parasite Plasmodium falciparum.","date":"2020","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/32867164","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["protein kinase 7","PfPK7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"33247522","id":"PMC_33247522","title":"Artificial Intelligence Applied to the Rapid Identification of New Antimalarial Candidates with Dual-Stage 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MEK inhibitors. PK7 lacks a typical MAPKK activation site in its T-loop, distinguishing it from canonical MAPKKs despite highest sequence similarity to the MAPKK3/6 subgroup in its C-terminal lobe and similarity to fungal PKA in its N-terminal region.\",\n      \"method\": \"Recombinant protein expression and in vitro kinase assay; inhibitor profiling; blastp sequence analysis\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro kinase assay with defined substrates and mutagenesis-equivalent negative controls (inability to phosphorylate MAPKs, inhibitor insensitivity), single lab but multiple orthogonal methods\",\n      \"pmids\": [\"15612927\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Genetic disruption of PK7 (pfpk7-) causes two distinct phenotypes: (1) reduced asexual growth rate in erythrocytes with fewer daughter merozoites per schizont, and (2) dramatic reduction in oocyst production in the mosquito vector. Both phenotypes are rescued by reintroduction of a functional pfpk7 gene, establishing PK7 as necessary for parasite proliferation during schizogony and for sporogony.\",\n      \"method\": \"Reverse genetics (gene disruption); phenotypic analysis of asexual growth and oocyst counts; genetic complementation\",\n      \"journal\": \"Eukaryotic cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined cellular phenotypes at two life-cycle stages, confirmed by genetic complementation, single lab with rigorous controls\",\n      \"pmids\": [\"18083830\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Crystal structure of PK7 reveals that the enzyme adopts a constitutively active conformation stabilized by an arginine residue in the activation loop that substitutes for the conserved phosphorylated residue that structures the activation loop in canonical kinases. The structure also reveals how extensive insertions are accommodated as excursions from the canonical eukaryotic protein kinase fold.\",\n      \"method\": \"X-ray crystallography; structural analysis of activation loop conformation\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional interpretation of activation mechanism; single lab but high-quality structural data with mechanistic consequence\",\n      \"pmids\": [\"18275814\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PK7 is required for melatonin signal transduction in P. falciparum: in pfpk7- parasites, melatonin treatment fails to (i) alter the ratio of asexual stages, (ii) induce a rise in cytoplasmic calcium, and (iii) up-regulate ubiquitin/proteasome system (UPS) gene transcription. Wild-type responses to melatonin are restored by complementation with a functional pfpk7 gene, placing PK7 upstream of calcium signaling and UPS gene regulation in the melatonin pathway.\",\n      \"method\": \"Gene knockout (pfpk7-) and genetic complementation; real-time PCR of UPS genes; calcium measurement; cell-cycle stage ratio analysis\",\n      \"journal\": \"Journal of pineal research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with multiple orthogonal readouts (calcium, transcription, cell-cycle staging) and genetic rescue, single lab\",\n      \"pmids\": [\"22348509\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Loss of PK7 in pfpk7- parasites causes major alterations in the expression of mitochondrial fission genes (FIS1, DYN1, DYN2) and abolishes melatonin-induced changes in fission protein expression. Mitochondrial functional characteristics (oxygen consumption) are profoundly altered in pfpk7- parasites, indicating PK7 plays a role in control of mitochondrial morphogenesis and maturation during intra-erythrocyte cell cycle progression.\",\n      \"method\": \"Gene knockout (pfpk7-); qRT-PCR of fission genes; MitoTracker staining; oxygen consumption measurement; GFP-mitochondrial matrix reporter\",\n      \"journal\": \"Journal of pineal research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — KO with multiple phenotypic readouts (transcription, morphology, respiration) but no direct biochemical link between PK7 and fission machinery; single lab\",\n      \"pmids\": [\"29480948\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Comparative quantitative phosphoproteomics of wild-type vs. pfpk7- parasites at schizont and segmenter stages identified 146 proteins with 239 phosphorylation sites showing reduced phosphorylation in the absence of PK7, and three phosphorylation motifs down-regulated in both stages. Direct in vitro kinase assays confirmed PK7 phosphorylates three of these candidate substrates, while many others showed indirect reduction in phosphorylation, revealing both direct substrates and downstream/compensatory signaling effects.\",\n      \"method\": \"Isobaric tag-based quantitative phosphoproteomics (TMT); in vitro kinase assay with candidate substrates; gene knockout (pfpk7-)\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — phosphoproteomics combined with direct in vitro kinase assay validation of substrates, multiple orthogonal methods in one study, single lab\",\n      \"pmids\": [\"29678115\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PfMORC expression is severely affected in pfpk7- parasites following melatonin treatment, placing PK7 upstream of PfMORC in the melatonin signaling pathway that regulates asexual stage synchronization.\",\n      \"method\": \"Gene knockout (pfpk7-); real-time expression assay of PfMORC; melatonin treatment\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — epistasis inferred from KO transcriptional readout, single lab, no direct biochemical interaction shown between PK7 and PfMORC\",\n      \"pmids\": [\"33479315\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    }\n  ],\n  \"current_model\": \"PK7 (PF3D7_0213400) is an atypical, constitutively active orphan kinase whose activation loop arginine substitutes for the canonical phosphorylated residue; it phosphorylates diverse substrates (identified by phosphoproteomics and direct in vitro assay) but not the P. falciparum MAPK homologues, and functions upstream of calcium signaling, ubiquitin/proteasome gene regulation, and PfMORC expression in the melatonin transduction pathway, while also being required for schizont-stage merozoite production and mosquito-stage oocyst development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PK7 (PF3D7_0213400) is an atypical orphan protein kinase of P. falciparum that governs parasite proliferation and melatonin signal transduction across the life cycle [#1, #3]. It is a constitutively active enzyme: its crystal structure shows an arginine residue in the activation loop substituting for the conserved phosphorylated residue that normally structures this region in canonical kinases, and it accommodates large insertions as excursions from the eukaryotic protein kinase fold [#2]. Recombinant PK7 phosphorylates diverse substrates in vitro but does not phosphorylate the P. falciparum MAPK homologues PfMAP1 and PfMAP2 and is insensitive to PKA and MEK inhibitors, distinguishing it from a canonical MAPKK despite C-terminal similarity to the MAPKK3/6 subgroup and N-terminal similarity to fungal PKA [#0]. Quantitative phosphoproteomics of pfpk7-null parasites identified 146 proteins with reduced phosphorylation and confirmed three of these as direct in vitro substrates, defining both direct targets and downstream signaling effects [#5]. Genetically, PK7 is required for schizogony, producing fewer daughter merozoites per schizont when disrupted, and for mosquito-stage oocyst formation, with both phenotypes rescued by complementation [#1]. Functionally, PK7 acts upstream in the melatonin transduction pathway, being necessary for melatonin-induced cytoplasmic calcium rise, up-regulation of ubiquitin/proteasome system genes, and PfMORC expression, and it also influences expression of mitochondrial fission genes and mitochondrial respiration during intra-erythrocytic development [#3, #4, #6]. No direct biochemical link between PK7 and the mitochondrial fission machinery or PfMORC has been established in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Whether PK7, annotated by sequence as MAPKK-like, actually functions as a MAP kinase kinase was unknown; the biochemistry showed it is an active kinase but not a functional MAPKK.\",\n      \"evidence\": \"Recombinant kinase assay with defined substrates, inhibitor profiling, and blastp analysis in P. falciparum\",\n      \"pmids\": [\"15612927\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological substrates not identified\", \"Lacks canonical MAPKK activation site — activation mechanism unexplained at this stage\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"The cellular requirement for PK7 was unknown; gene disruption established that it is needed for asexual schizogony and for mosquito-stage sporogony.\",\n      \"evidence\": \"Reverse-genetic knockout with phenotyping and genetic complementation in P. falciparum\",\n      \"pmids\": [\"18083830\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular pathway linking PK7 to merozoite number and oocyst formation not defined\", \"Substrates driving these phenotypes unidentified\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"The activation state of an orphan kinase lacking a canonical T-loop phosphosite was unclear; the structure revealed a constitutively active conformation stabilized by an activation-loop arginine.\",\n      \"evidence\": \"X-ray crystallography and structural analysis of activation-loop conformation in P. falciparum PK7\",\n      \"pmids\": [\"18275814\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No substrate-bound or inhibitor-bound structures\", \"Regulation of an already-active kinase in vivo unresolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Where PK7 sits in a signaling pathway was unknown; knockout placed it upstream of melatonin-induced calcium signaling and ubiquitin/proteasome gene regulation.\",\n      \"evidence\": \"pfpk7- knockout and complementation with calcium measurement, UPS gene qPCR, and cell-cycle staging in P. falciparum\",\n      \"pmids\": [\"22348509\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct substrates transmitting the melatonin signal not identified\", \"Mechanism coupling PK7 to calcium mobilization unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether PK7 influences organellar biogenesis was unknown; knockout showed altered mitochondrial fission gene expression and respiration during the intra-erythrocytic cycle.\",\n      \"evidence\": \"pfpk7- knockout with fission-gene qRT-PCR, MitoTracker/GFP reporter imaging, and oxygen consumption in P. falciparum\",\n      \"pmids\": [\"29480948\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct biochemical link between PK7 and fission machinery (FIS1, DYN1, DYN2)\", \"Effects may be indirect downstream consequences of the growth defect\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The direct substrates of PK7 were undefined; comparative phosphoproteomics of null parasites mapped PK7-dependent phosphosites and validated three direct substrates in vitro.\",\n      \"evidence\": \"TMT quantitative phosphoproteomics of wild-type vs pfpk7- schizonts/segmenters plus in vitro kinase assays in P. falciparum\",\n      \"pmids\": [\"29678115\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Most of the 146 affected proteins are indirect and their upstream kinases unresolved\", \"Identity/function of the three validated substrates not developmentally contextualized\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Whether PK7 controls downstream chromatin/transcriptional regulators in the melatonin pathway was unknown; knockout showed PfMORC expression is impaired after melatonin treatment.\",\n      \"evidence\": \"pfpk7- knockout with real-time PfMORC expression assay following melatonin treatment in P. falciparum 3D7\",\n      \"pmids\": [\"33479315\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Epistasis inferred from transcription only — no direct PK7–PfMORC biochemical interaction\", \"Intermediate steps between PK7 and PfMORC regulation unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The physiological substrate(s) that mechanistically link PK7 to calcium mobilization, UPS/PfMORC gene regulation, merozoite production, and oocyst development remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate mapped to a specific downstream phenotype\", \"No interaction partner or scaffold identified\", \"How a constitutively active kinase is signal-regulated by melatonin is unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004672\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"GO:0106310\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0007165\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0019722\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0000266\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Constitutively active orphan kinase; activation-loop arginine substitutes for the canonical phosphorylated activation residue [#2]\",\n      \"Does not phosphorylate P. falciparum MAPK homologues PfMAP1/PfMAP2 and is insensitive to PKA and MEK inhibitors [#0]\",\n      \"Required for schizont-stage merozoite production and mosquito-stage oocyst development [#1]\",\n      \"Acts upstream of melatonin-induced calcium rise, UPS gene transcription, and PfMORC expression [#3, #6]\",\n      \"Influences mitochondrial fission gene expression and respiration during intra-erythrocytic development [#4]\",\n      \"Three direct in vitro substrates validated from phosphoproteomics of pfpk7- parasites [#5]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0213400","name":null,"product":"protein kinase 7","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0310300","name":null,"product":"protein kinase 7","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0407600","name":null,"product":"protein kinase 7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"PK7","evaluation":null}