{"gene":"PF3D7_1362200","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2012,"finding":"Recombinant RUVB3 (PfRuvB3) possesses ssDNA-dependent ATPase activity; Walker motif A, established by truncation mutagenesis, is essential for this enzymatic activity. Immunodepletion assays confirmed that the ATPase activity is attributable to the RUVB3 protein itself.","method":"In vitro ATPase assay with recombinant protein, truncated-derivative mutagenesis, immunodepletion assay","journal":"Molecular and biochemical parasitology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical reconstitution with active-site mutagenesis and immunodepletion, single lab with multiple orthogonal methods","pmids":["22705314"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"Endogenous RUVB3 from P. falciparum lysate exhibits ATPase activity and some DNA helicase activity.","method":"Biochemical assay of endogenous protein from parasite lysate","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — endogenous protein assay, single lab, single method","pmids":["22705314"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"RUVB3 localizes to the nuclear region during intraerythrocytic schizont stages; upon merozoite release from schizont, RUVB3 relocalizes to a subnuclear compartment. Co-localization with the nucleolar marker PfNop1 indicates RUVB3 resides in a discrete nuclear/nucleolar compartment.","method":"Confocal immunofluorescence microscopy with anti-RUVB3 antibody and anti-PfNop1 (nucleolar marker)","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct immunofluorescence localization with a nucleolar co-localization control, single lab","pmids":["22705314"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"RUVB3 forms a physical complex with PfRuvB2 (but not with PfRuvB1) as shown by immunopurification of the RUVB3 complex followed by confirmation of PfRuvB2 presence, and by in vitro interaction assay. The presence of RUVB3 in the PfRuvB2 helicase reaction significantly increases PfRuvB2 helicase activity, acting as a modulator; the RUVB2/RUVB3 complex preferentially translocates and unwinds DNA in the 5′-to-3′ direction.","method":"Immunopurification of endogenous RUVB3 complex, in vitro protein interaction assay, in vitro helicase activity assay with and without RUVB3","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — immunopurification, in vitro interaction, and functional helicase stimulation assay; multiple orthogonal methods in single lab","pmids":["24161468"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"Recombinant RUVB3 from P. falciparum strain K1 possesses both ATP-dependent DNA helicase and ATPase activities. Helicase activity requires divalent cations (Cu²⁺, Mg²⁺, Ni²⁺, or Zn²⁺) and ATP or dATP, is inhibited by high NaCl (>100 mM), and cannot act on blunt-ended duplex DNA. ATPase activity is stimulated by both single- and double-stranded DNA. Known helicase inhibitors doxorubicin, daunorubicin, and netropsin inhibit RUVB3 activity.","method":"Heterologous expression and affinity purification of recombinant protein; in vitro helicase and ATPase assays with cofactor variation; inhibitor assays; western blot and tandem mass spectrometry identity confirmation","journal":"Malaria journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical reconstitution with multiple substrate and cofactor conditions, identity verified by MS, single lab with multiple orthogonal methods","pmids":["27809838"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"K1"}]},{"year":2018,"finding":"RUVB3 (PfRUVBL3) possesses DNA cleavage activity that is dependent on its insertion domain, distinct from its ATPase and oligomerization activities. RUVB3 physically interacts with the essential chromatin remodeling protein PfMYST (a HAT), and together they co-localize with H3K9me1 histone in the parasitophorous vacuole during the ring stage, suggesting involvement in chromatin remodeling and gene transcription.","method":"In vitro DNA cleavage assay with domain-deletion constructs; co-immunoprecipitation / interaction assay with PfMYST; immunofluorescence co-localization with H3K9me1; ATPase and oligomerization assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — DNA cleavage domain mapping by deletion constructs, Co-IP for interaction, IF co-localization; single lab but multiple orthogonal methods","pmids":["30026605"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"RUVB3 is expressed throughout all intraerythrocytic cycle stages with varied subcellular localization during the IDC (ring, trophozoite, schizont stages).","method":"Immunofluorescence microscopy across intraerythrocytic developmental stages","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single-lab immunofluorescence, no functional perturbation linked to localization change","pmids":["30026605"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1362200 (RUVB3) is a nuclear AAA+-family ATPase/helicase that exhibits ssDNA-dependent ATPase activity (requiring an intact Walker motif A), ATP- and divalent-cation-dependent DNA helicase activity, and a novel insertion-domain-dependent DNA cleavage activity; it forms a complex specifically with PfRuvB2 (not PfRuvB1) and stimulates PfRuvB2 helicase activity in a 5′-to-3′ direction, and also interacts with the chromatin remodeling HAT protein PfMYST, co-localizing with H3K9me1 in the parasitophorous vacuole during ring stage, suggesting roles in intraerythrocytic schizogony, chromatin remodeling, and gene transcription."},"narrative":{"mechanistic_narrative":"PF3D7_1362200 (RUVB3) is a nuclear AAA+-family DNA helicase/ATPase of Plasmodium falciparum implicated in DNA transactions and chromatin remodeling across the intraerythrocytic developmental cycle [PMID:22705314, PMID:27809838, PMID:30026605]. Recombinant RUVB3 possesses ssDNA-dependent ATPase activity that depends on an intact Walker motif A, and it exhibits ATP- and divalent-cation-dependent DNA helicase activity that is stimulated by both single- and double-stranded DNA yet inactive on blunt-ended duplex; its enzymatic activity is inhibited by the helicase inhibitors doxorubicin, daunorubicin, and netropsin [PMID:22705314, PMID:27809838]. RUVB3 forms a specific physical complex with PfRuvB2 (but not PfRuvB1) and acts as a modulator that stimulates PfRuvB2 helicase activity, the complex preferentially unwinding DNA in the 5'-to-3' direction [PMID:24161468]. Beyond its helicase role, RUVB3 carries an insertion-domain-dependent DNA cleavage activity distinct from its ATPase and oligomerization functions, and it interacts with the chromatin-remodeling histone acetyltransferase PfMYST, co-localizing with H3K9me1, linking it to chromatin remodeling and gene transcription [PMID:30026605]. RUVB3 localizes to a discrete nuclear/nucleolar compartment (co-localizing with the nucleolar marker PfNop1) during schizont stages and shows stage-varied subcellular distribution across the intraerythrocytic cycle [PMID:22705314, PMID:30026605]. The physiological consequences of RUVB3 activity in vivo, and the significance of its parasitophorous-vacuole co-localization with PfMYST/H3K9me1, have not been resolved by loss-of-function studies in the available corpus.","teleology":[{"year":2012,"claim":"Whether the RUVB3 polypeptide itself is an active ATPase was unknown; assigning the catalytic activity to the protein and to a specific motif established it as a bona fide AAA+ enzyme rather than a passive complex subunit.","evidence":"In vitro ATPase assay of recombinant protein with Walker-A truncation mutagenesis and immunodepletion of endogenous protein","pmids":["22705314"],"confidence":"High","gaps":["Helicase directionality and substrate preference of RUVB3 alone not defined here","No in vivo perturbation linking the ATPase activity to parasite phenotype"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"Localizing endogenous RUVB3 placed its enzymatic activity in a defined subcellular context, showing it occupies a nuclear/nucleolar compartment that shifts upon merozoite release.","evidence":"Confocal immunofluorescence with anti-RUVB3 and nucleolar marker PfNop1","pmids":["22705314"],"confidence":"Medium","gaps":["Functional meaning of the schizont-to-subnuclear relocalization not tested","Single-lab immunofluorescence without perturbation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"The question of RUVB3's partner within the RuvB family was resolved by demonstrating a selective RUVB3–PfRuvB2 complex, and by showing RUVB3 functionally modulates its partner's helicase activity and directional unwinding.","evidence":"Immunopurification of endogenous RUVB3 complex, in vitro interaction assay, and helicase assays with/without RUVB3","pmids":["24161468"],"confidence":"High","gaps":["Stoichiometry and structural basis of the RUVB2/RUVB3 complex unknown","Why PfRuvB1 is excluded not explained mechanistically","In vivo requirement of the complex untested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"claim":"The cofactor and substrate requirements of RUVB3's intrinsic helicase activity were defined, characterizing it as an ATP/divalent-cation-dependent enzyme and identifying small-molecule inhibitors.","evidence":"Heterologous expression (strain K1), in vitro helicase/ATPase assays with cofactor variation and inhibitor testing, identity confirmed by mass spectrometry","pmids":["27809838"],"confidence":"High","gaps":["Physiological DNA substrate in the parasite unknown","Inhibitor selectivity over host helicases not established"],"attribution":[{"species":"Plasmodium falciparum","strain":"K1"}]},{"year":2018,"claim":"A previously unrecognized DNA cleavage activity mapped to the insertion domain, plus a physical link to the chromatin-modifying HAT PfMYST, extended RUVB3's role beyond DNA unwinding toward chromatin remodeling and transcription.","evidence":"In vitro DNA cleavage assay with domain-deletion constructs, Co-IP with PfMYST, and IF co-localization with H3K9me1","pmids":["30026605"],"confidence":"Medium","gaps":["Biological role of the DNA cleavage activity in vivo unknown","PfMYST interaction from single Co-IP without reciprocal validation","Functional consequence of H3K9me1 co-localization in the parasitophorous vacuole untested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"RUVB3 is expressed across all intraerythrocytic stages with varying localization, indicating persistent but stage-modulated function during the developmental cycle.","evidence":"Immunofluorescence microscopy across ring, trophozoite, and schizont stages","pmids":["30026605"],"confidence":"Medium","gaps":["No functional perturbation tied to the localization changes","Stage-specific interaction partners not mapped"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The in vivo essentiality and physiological function of RUVB3 during schizogony, chromatin remodeling, and transcription remain unresolved.","evidence":"No loss-of-function or genetic perturbation study present in the corpus","pmids":[],"confidence":"Low","gaps":["No knockout/knockdown phenotype","No structural model of RUVB3 or its complexes","Genomic targets of RUVB3 helicase/cleavage activity unidentified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["RUVB3/PfRuvB2 helicase complex"],"partners":["PFRUVB2","PFMYST (HISTONE ACETYLTRANSFERASE)"],"other_free_text":["ssDNA- and dsDNA-stimulated ATPase activity requiring intact Walker motif A [#0, #4]","Helicase activity requires ATP/dATP and divalent cations (Cu2+, Mg2+, Ni2+, Zn2+), inhibited by >100 mM NaCl, and inactive on blunt-ended duplex DNA [#4]","Inhibited by helicase inhibitors doxorubicin, daunorubicin, and netropsin [#4]","RUVB2/RUVB3 complex preferentially unwinds DNA 5'-to-3'; RUVB3 stimulates PfRuvB2 helicase activity [#3]","DNA cleavage activity mapped to the insertion domain, distinct from ATPase and oligomerization [#5]","Co-localizes with H3K9me1 histone [#5]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"22705314","id":"PMC_22705314","title":"Novel RuvB nuclear ATPase is specific to intraerythrocytic mitosis during schizogony of Plasmodium falciparum.","date":"2012","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/22705314","citation_count":15,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RUVB3","PfRUVB3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23219504","id":"PMC_23219504","title":"Plasmodium falciparum RuvB1 is an active DNA helicase and translocates in the 5'-3' direction.","date":"2012","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/23219504","citation_count":14,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRUVB3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24161468","id":"PMC_24161468","title":"Plasmodium falciparum RuvB2 translocates in 5'-3' direction, relocalizes during schizont stage and its enzymatic activities are up regulated by RuvB3 of the same complex.","date":"2013","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/24161468","citation_count":12,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RUVB3","PfRUVB3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"30026605","id":"PMC_30026605","title":"Plasmodium falciparum RUVBL3 protein: a novel DNA modifying enzyme and an interacting partner of essential HAT protein MYST.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30026605","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27809838","id":"PMC_27809838","title":"Characterization of Plasmodium falciparum ATP-dependent DNA helicase RuvB3.","date":"2016","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/27809838","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RUVB3","PfRUVB3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5509,"output_tokens":2121,"usd":0.024171,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7329,"output_tokens":3323,"usd":0.05986,"stage2_stop_reason":"end_turn"},"total_usd":0.084031,"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\": 2012,\n      \"finding\": \"Recombinant RUVB3 (PfRuvB3) possesses ssDNA-dependent ATPase activity; Walker motif A, established by truncation mutagenesis, is essential for this enzymatic activity. Immunodepletion assays confirmed that the ATPase activity is attributable to the RUVB3 protein itself.\",\n      \"method\": \"In vitro ATPase assay with recombinant protein, truncated-derivative mutagenesis, immunodepletion assay\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical reconstitution with active-site mutagenesis and immunodepletion, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"22705314\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Endogenous RUVB3 from P. falciparum lysate exhibits ATPase activity and some DNA helicase activity.\",\n      \"method\": \"Biochemical assay of endogenous protein from parasite lysate\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — endogenous protein assay, single lab, single method\",\n      \"pmids\": [\"22705314\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RUVB3 localizes to the nuclear region during intraerythrocytic schizont stages; upon merozoite release from schizont, RUVB3 relocalizes to a subnuclear compartment. Co-localization with the nucleolar marker PfNop1 indicates RUVB3 resides in a discrete nuclear/nucleolar compartment.\",\n      \"method\": \"Confocal immunofluorescence microscopy with anti-RUVB3 antibody and anti-PfNop1 (nucleolar marker)\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct immunofluorescence localization with a nucleolar co-localization control, single lab\",\n      \"pmids\": [\"22705314\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RUVB3 forms a physical complex with PfRuvB2 (but not with PfRuvB1) as shown by immunopurification of the RUVB3 complex followed by confirmation of PfRuvB2 presence, and by in vitro interaction assay. The presence of RUVB3 in the PfRuvB2 helicase reaction significantly increases PfRuvB2 helicase activity, acting as a modulator; the RUVB2/RUVB3 complex preferentially translocates and unwinds DNA in the 5′-to-3′ direction.\",\n      \"method\": \"Immunopurification of endogenous RUVB3 complex, in vitro protein interaction assay, in vitro helicase activity assay with and without RUVB3\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — immunopurification, in vitro interaction, and functional helicase stimulation assay; multiple orthogonal methods in single lab\",\n      \"pmids\": [\"24161468\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Recombinant RUVB3 from P. falciparum strain K1 possesses both ATP-dependent DNA helicase and ATPase activities. Helicase activity requires divalent cations (Cu²⁺, Mg²⁺, Ni²⁺, or Zn²⁺) and ATP or dATP, is inhibited by high NaCl (>100 mM), and cannot act on blunt-ended duplex DNA. ATPase activity is stimulated by both single- and double-stranded DNA. Known helicase inhibitors doxorubicin, daunorubicin, and netropsin inhibit RUVB3 activity.\",\n      \"method\": \"Heterologous expression and affinity purification of recombinant protein; in vitro helicase and ATPase assays with cofactor variation; inhibitor assays; western blot and tandem mass spectrometry identity confirmation\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical reconstitution with multiple substrate and cofactor conditions, identity verified by MS, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27809838\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"K1\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RUVB3 (PfRUVBL3) possesses DNA cleavage activity that is dependent on its insertion domain, distinct from its ATPase and oligomerization activities. RUVB3 physically interacts with the essential chromatin remodeling protein PfMYST (a HAT), and together they co-localize with H3K9me1 histone in the parasitophorous vacuole during the ring stage, suggesting involvement in chromatin remodeling and gene transcription.\",\n      \"method\": \"In vitro DNA cleavage assay with domain-deletion constructs; co-immunoprecipitation / interaction assay with PfMYST; immunofluorescence co-localization with H3K9me1; ATPase and oligomerization assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — DNA cleavage domain mapping by deletion constructs, Co-IP for interaction, IF co-localization; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"30026605\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RUVB3 is expressed throughout all intraerythrocytic cycle stages with varied subcellular localization during the IDC (ring, trophozoite, schizont stages).\",\n      \"method\": \"Immunofluorescence microscopy across intraerythrocytic developmental stages\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single-lab immunofluorescence, no functional perturbation linked to localization change\",\n      \"pmids\": [\"30026605\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1362200 (RUVB3) is a nuclear AAA+-family ATPase/helicase that exhibits ssDNA-dependent ATPase activity (requiring an intact Walker motif A), ATP- and divalent-cation-dependent DNA helicase activity, and a novel insertion-domain-dependent DNA cleavage activity; it forms a complex specifically with PfRuvB2 (not PfRuvB1) and stimulates PfRuvB2 helicase activity in a 5′-to-3′ direction, and also interacts with the chromatin remodeling HAT protein PfMYST, co-localizing with H3K9me1 in the parasitophorous vacuole during ring stage, suggesting roles in intraerythrocytic schizogony, chromatin remodeling, and gene transcription.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1362200 (RUVB3) is a nuclear AAA+-family DNA helicase/ATPase of Plasmodium falciparum implicated in DNA transactions and chromatin remodeling across the intraerythrocytic developmental cycle [#0, #4, #5]. Recombinant RUVB3 possesses ssDNA-dependent ATPase activity that depends on an intact Walker motif A, and it exhibits ATP- and divalent-cation-dependent DNA helicase activity that is stimulated by both single- and double-stranded DNA yet inactive on blunt-ended duplex; its enzymatic activity is inhibited by the helicase inhibitors doxorubicin, daunorubicin, and netropsin [#0, #4]. RUVB3 forms a specific physical complex with PfRuvB2 (but not PfRuvB1) and acts as a modulator that stimulates PfRuvB2 helicase activity, the complex preferentially unwinding DNA in the 5'-to-3' direction [#3]. Beyond its helicase role, RUVB3 carries an insertion-domain-dependent DNA cleavage activity distinct from its ATPase and oligomerization functions, and it interacts with the chromatin-remodeling histone acetyltransferase PfMYST, co-localizing with H3K9me1, linking it to chromatin remodeling and gene transcription [#5]. RUVB3 localizes to a discrete nuclear/nucleolar compartment (co-localizing with the nucleolar marker PfNop1) during schizont stages and shows stage-varied subcellular distribution across the intraerythrocytic cycle [#2, #6]. The physiological consequences of RUVB3 activity in vivo, and the significance of its parasitophorous-vacuole co-localization with PfMYST/H3K9me1, have not been resolved by loss-of-function studies in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Whether the RUVB3 polypeptide itself is an active ATPase was unknown; assigning the catalytic activity to the protein and to a specific motif established it as a bona fide AAA+ enzyme rather than a passive complex subunit.\",\n      \"evidence\": \"In vitro ATPase assay of recombinant protein with Walker-A truncation mutagenesis and immunodepletion of endogenous protein\",\n      \"pmids\": [\"22705314\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Helicase directionality and substrate preference of RUVB3 alone not defined here\", \"No in vivo perturbation linking the ATPase activity to parasite phenotype\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Localizing endogenous RUVB3 placed its enzymatic activity in a defined subcellular context, showing it occupies a nuclear/nucleolar compartment that shifts upon merozoite release.\",\n      \"evidence\": \"Confocal immunofluorescence with anti-RUVB3 and nucleolar marker PfNop1\",\n      \"pmids\": [\"22705314\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional meaning of the schizont-to-subnuclear relocalization not tested\", \"Single-lab immunofluorescence without perturbation\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The question of RUVB3's partner within the RuvB family was resolved by demonstrating a selective RUVB3–PfRuvB2 complex, and by showing RUVB3 functionally modulates its partner's helicase activity and directional unwinding.\",\n      \"evidence\": \"Immunopurification of endogenous RUVB3 complex, in vitro interaction assay, and helicase assays with/without RUVB3\",\n      \"pmids\": [\"24161468\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and structural basis of the RUVB2/RUVB3 complex unknown\", \"Why PfRuvB1 is excluded not explained mechanistically\", \"In vivo requirement of the complex untested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"The cofactor and substrate requirements of RUVB3's intrinsic helicase activity were defined, characterizing it as an ATP/divalent-cation-dependent enzyme and identifying small-molecule inhibitors.\",\n      \"evidence\": \"Heterologous expression (strain K1), in vitro helicase/ATPase assays with cofactor variation and inhibitor testing, identity confirmed by mass spectrometry\",\n      \"pmids\": [\"27809838\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological DNA substrate in the parasite unknown\", \"Inhibitor selectivity over host helicases not established\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"K1\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"A previously unrecognized DNA cleavage activity mapped to the insertion domain, plus a physical link to the chromatin-modifying HAT PfMYST, extended RUVB3's role beyond DNA unwinding toward chromatin remodeling and transcription.\",\n      \"evidence\": \"In vitro DNA cleavage assay with domain-deletion constructs, Co-IP with PfMYST, and IF co-localization with H3K9me1\",\n      \"pmids\": [\"30026605\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Biological role of the DNA cleavage activity in vivo unknown\", \"PfMYST interaction from single Co-IP without reciprocal validation\", \"Functional consequence of H3K9me1 co-localization in the parasitophorous vacuole untested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"RUVB3 is expressed across all intraerythrocytic stages with varying localization, indicating persistent but stage-modulated function during the developmental cycle.\",\n      \"evidence\": \"Immunofluorescence microscopy across ring, trophozoite, and schizont stages\",\n      \"pmids\": [\"30026605\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional perturbation tied to the localization changes\", \"Stage-specific interaction partners not mapped\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The in vivo essentiality and physiological function of RUVB3 during schizogony, chromatin remodeling, and transcription remain unresolved.\",\n      \"evidence\": \"No loss-of-function or genetic perturbation study present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No knockout/knockdown phenotype\", \"No structural model of RUVB3 or its complexes\", \"Genomic targets of RUVB3 helicase/cleavage activity unidentified\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0043141\", \"supporting_discovery_ids\": [1, 3, 4]},\n      {\"term_id\": \"GO:0004003\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0016887\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0043142\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0004518\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0003697\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0020020\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006338\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0006355\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [\n      \"RUVB3/PfRuvB2 helicase complex\"\n    ],\n    \"partners\": [\n      \"PfRuvB2\",\n      \"PfMYST (histone acetyltransferase)\"\n    ],\n    \"other_free_text\": [\n      \"ssDNA- and dsDNA-stimulated ATPase activity requiring intact Walker motif A [#0, #4]\",\n      \"Helicase activity requires ATP/dATP and divalent cations (Cu2+, Mg2+, Ni2+, Zn2+), inhibited by >100 mM NaCl, and inactive on blunt-ended duplex DNA [#4]\",\n      \"Inhibited by helicase inhibitors doxorubicin, daunorubicin, and netropsin [#4]\",\n      \"RUVB2/RUVB3 complex preferentially unwinds DNA 5'-to-3'; RUVB3 stimulates PfRuvB2 helicase activity [#3]\",\n      \"DNA cleavage activity mapped to the insertion domain, distinct from ATPase and oligomerization [#5]\",\n      \"Co-localizes with H3K9me1 histone [#5]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1362200","name":null,"product":"RuvB-like helicase 3","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1138200","name":null,"product":"RuvB-like helicase 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1109100","name":null,"product":"RuvB-like helicase 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RUVB3","evaluation":null}