{"gene":"PF3D7_1365600","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2016,"finding":"PF3D7_1365600 (TOP6B / PfTopoVIB) forms homodimers and heteromers with PfTopoVIA (the A subunit), as demonstrated by yeast two-hybrid analysis. The TOP6B–TOP6A complex can decatenate DNA in an ATP- and Mg2+-dependent manner, as shown by a cell-free decatenation assay. TOP6B alone cannot rescue the lethal phenotype of yeast ΔtopoII mutants, but TOP6B together with TOP6A can, establishing that both subunits are required for type II topoisomerase activity. Decatenation activity is specifically abrogated by anti-TOP6B antibody. Radicicol and etoposide inhibit this decatenation activity, whereas the gyrase inhibitor novobiocin does not.","method":"Yeast two-hybrid (protein–protein interaction), heterologous expression in Saccharomyces cerevisiae, yeast ΔtopoII complementation (genetic epistasis), cell-free decatenation assay, antibody-mediated inhibition","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal yeast two-hybrid, functional complementation epistasis, and biochemical decatenation assay in a single lab with multiple orthogonal methods; no in vitro reconstitution with purified recombinant protein","pmids":["27303712"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1986,"finding":"Topoisomerase II purified from Plasmodium berghei consists of two subunits of approximately 160 kDa each, is ATP- and Mg2+-dependent, and supports relaxation, unknotting, decatenation, and catenation reactions similar to eukaryotic topoisomerases II. Ellipticine derivatives were the most active inhibitors; antimalarial drugs currently used clinically were poor inhibitors and did not stimulate double-stranded DNA cleavage activity, suggesting Plasmodium topoisomerases are not good targets for these antimalarials.","method":"Biochemical purification from P. berghei-infected erythrocytes, in vitro relaxation/decatenation/catenation assays, drug inhibition assays","journal":"Biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — biochemical characterization of the native complex from P. berghei before molecular cloning; TOP6B identity of the subunits was not established at the gene level, single study","pmids":["3011062"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"PF3D7_1365600 (TOP6B) is the B subunit of the Plasmodium falciparum type II topoisomerase VI complex: it forms homodimers and heterodimerises with the A subunit (TOP6A), and the TOP6B–TOP6A complex performs ATP- and Mg2+-dependent DNA decatenation; TOP6B alone is catalytically inactive, and the complex is specifically inhibited by radicicol and etoposide but not by novobiocin."},"narrative":{"mechanistic_narrative":"PF3D7_1365600 (TOP6B) is the B subunit of the Plasmodium falciparum type II topoisomerase VI, functioning in ATP-dependent DNA decatenation [PMID:27303712]. It self-associates into homodimers and heterodimerises with the A subunit (TOP6A), and only the assembled TOP6B–TOP6A complex reconstitutes type II topoisomerase activity: the complex decatenates DNA in an ATP- and Mg2+-dependent manner and rescues the lethality of yeast ΔtopoII mutants, whereas TOP6B alone is catalytically inactive and cannot complement [PMID:27303712]. Anti-TOP6B antibody abrogates decatenation, and the activity is inhibited by radicicol and etoposide but not by the gyrase inhibitor novobiocin [PMID:27303712]. Beyond this heterodimeric decatenation function established for the recombinant/heterologous system in [PMID:27303712], no further mechanistic detail—structure, in vitro reconstitution with purified protein, or in-parasite phenotype—has been characterized for PF3D7_1365600 in the available corpus.","teleology":[{"year":2016,"claim":"Whether PF3D7_1365600 encodes a functional topoisomerase subunit and how it partners with the A subunit was unknown; this work established TOP6B as a homodimer-forming, A-subunit-dependent component of an active type II topoisomerase.","evidence":"Yeast two-hybrid interaction mapping, ΔtopoII complementation epistasis, and cell-free ATP/Mg2+-dependent decatenation assay with antibody and drug inhibition in P. falciparum-derived subunits","pmids":["27303712"],"confidence":"Medium","gaps":["No in vitro reconstitution with purified recombinant TOP6B protein","The catalytic contribution of TOP6B versus TOP6A within the complex is not dissected","No in-parasite genetic essentiality or knockout phenotype for PF3D7_1365600"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":1986,"claim":"Before gene-level identification, the question was whether Plasmodium possesses a eukaryotic-type topoisomerase II activity and whether antimalarials target it; a two-subunit, ATP/Mg2+-dependent activity was purified from P. berghei but was not attributed to any specific gene.","evidence":"Biochemical purification from P. berghei-infected erythrocytes with relaxation/unknotting/decatenation/catenation and drug inhibition assays","pmids":["3011062"],"confidence":"Low","gaps":["The purified subunits were not mapped to TOP6B at the gene level, so this activity cannot be assigned to PF3D7_1365600","Performed in P. berghei, not P. falciparum","No molecular identity of the ~160 kDa subunits established"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"Whether TOP6B contributes catalytically or structurally within the heterodimer, its atomic structure, and its role in parasite replication in vivo remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of TOP6B or the TOP6B–TOP6A complex","No in vitro reconstitution with fully purified recombinant subunits","No genetic dissection of TOP6B function during the P. falciparum life cycle"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Type II topoisomerase VI (TOP6B–TOP6A heterodimer)","TOP6B homodimer"],"partners":["TOP6A (PFTOPOVIA, A SUBUNIT)"],"other_free_text":["Decatenation activity of the TOP6B–TOP6A complex is inhibited by radicicol and etoposide but not by novobiocin [#0]","TOP6B alone cannot complement yeast ΔtopoII lethality; both TOP6B and TOP6A are required for activity [#0]","A native two-subunit, ATP/Mg2+-dependent topoisomerase II activity was purified from P. berghei but not assigned to PF3D7_1365600 at the gene level [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"3011062","id":"PMC_3011062","title":"Purification and characterization of Plasmodium berghei DNA topoisomerases I and II: drug action, inhibition of decatenation and relaxation, and stimulation of DNA cleavage.","date":"1986","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/3011062","citation_count":77,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"3088783","id":"PMC_3088783","title":"Rapid repeated DNA replication during microgametogenesis and DNA synthesis in young zygotes of Plasmodium berghei.","date":"1986","source":"Transactions of the Royal Society of Tropical Medicine and Hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/3088783","citation_count":61,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15948708","id":"PMC_15948708","title":"DNA-[adenine] methylation in lower eukaryotes.","date":"2005","source":"Biochemistry. Biokhimiia","url":"https://pubmed.ncbi.nlm.nih.gov/15948708","citation_count":42,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"2892060","id":"PMC_2892060","title":"From Laveran's discovery to DNA probes: new trends in diagnosis of malaria.","date":"1987","source":"Lancet (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/2892060","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27303712","id":"PMC_27303712","title":"Radicicol-Mediated Inhibition of Topoisomerase VIB-VIA Activity of the Human Malaria Parasite Plasmodium falciparum.","date":"2016","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/27303712","citation_count":20,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4659,"output_tokens":885,"usd":0.013626,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5600,"output_tokens":1842,"usd":0.037025,"stage2_stop_reason":"end_turn"},"total_usd":0.050651,"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\": 2016,\n      \"finding\": \"PF3D7_1365600 (TOP6B / PfTopoVIB) forms homodimers and heteromers with PfTopoVIA (the A subunit), as demonstrated by yeast two-hybrid analysis. The TOP6B–TOP6A complex can decatenate DNA in an ATP- and Mg2+-dependent manner, as shown by a cell-free decatenation assay. TOP6B alone cannot rescue the lethal phenotype of yeast ΔtopoII mutants, but TOP6B together with TOP6A can, establishing that both subunits are required for type II topoisomerase activity. Decatenation activity is specifically abrogated by anti-TOP6B antibody. Radicicol and etoposide inhibit this decatenation activity, whereas the gyrase inhibitor novobiocin does not.\",\n      \"method\": \"Yeast two-hybrid (protein–protein interaction), heterologous expression in Saccharomyces cerevisiae, yeast ΔtopoII complementation (genetic epistasis), cell-free decatenation assay, antibody-mediated inhibition\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal yeast two-hybrid, functional complementation epistasis, and biochemical decatenation assay in a single lab with multiple orthogonal methods; no in vitro reconstitution with purified recombinant protein\",\n      \"pmids\": [\"27303712\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 1986,\n      \"finding\": \"Topoisomerase II purified from Plasmodium berghei consists of two subunits of approximately 160 kDa each, is ATP- and Mg2+-dependent, and supports relaxation, unknotting, decatenation, and catenation reactions similar to eukaryotic topoisomerases II. Ellipticine derivatives were the most active inhibitors; antimalarial drugs currently used clinically were poor inhibitors and did not stimulate double-stranded DNA cleavage activity, suggesting Plasmodium topoisomerases are not good targets for these antimalarials.\",\n      \"method\": \"Biochemical purification from P. berghei-infected erythrocytes, in vitro relaxation/decatenation/catenation assays, drug inhibition assays\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — biochemical characterization of the native complex from P. berghei before molecular cloning; TOP6B identity of the subunits was not established at the gene level, single study\",\n      \"pmids\": [\"3011062\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1365600 (TOP6B) is the B subunit of the Plasmodium falciparum type II topoisomerase VI complex: it forms homodimers and heterodimerises with the A subunit (TOP6A), and the TOP6B–TOP6A complex performs ATP- and Mg2+-dependent DNA decatenation; TOP6B alone is catalytically inactive, and the complex is specifically inhibited by radicicol and etoposide but not by novobiocin.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1365600 (TOP6B) is the B subunit of the Plasmodium falciparum type II topoisomerase VI, functioning in ATP-dependent DNA decatenation [#0]. It self-associates into homodimers and heterodimerises with the A subunit (TOP6A), and only the assembled TOP6B–TOP6A complex reconstitutes type II topoisomerase activity: the complex decatenates DNA in an ATP- and Mg2+-dependent manner and rescues the lethality of yeast ΔtopoII mutants, whereas TOP6B alone is catalytically inactive and cannot complement [#0]. Anti-TOP6B antibody abrogates decatenation, and the activity is inhibited by radicicol and etoposide but not by the gyrase inhibitor novobiocin [#0]. Beyond this heterodimeric decatenation function established for the recombinant/heterologous system in [#0], no further mechanistic detail—structure, in vitro reconstitution with purified protein, or in-parasite phenotype—has been characterized for PF3D7_1365600 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Whether PF3D7_1365600 encodes a functional topoisomerase subunit and how it partners with the A subunit was unknown; this work established TOP6B as a homodimer-forming, A-subunit-dependent component of an active type II topoisomerase.\",\n      \"evidence\": \"Yeast two-hybrid interaction mapping, ΔtopoII complementation epistasis, and cell-free ATP/Mg2+-dependent decatenation assay with antibody and drug inhibition in P. falciparum-derived subunits\",\n      \"pmids\": [\"27303712\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in vitro reconstitution with purified recombinant TOP6B protein\",\n        \"The catalytic contribution of TOP6B versus TOP6A within the complex is not dissected\",\n        \"No in-parasite genetic essentiality or knockout phenotype for PF3D7_1365600\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 1986,\n      \"claim\": \"Before gene-level identification, the question was whether Plasmodium possesses a eukaryotic-type topoisomerase II activity and whether antimalarials target it; a two-subunit, ATP/Mg2+-dependent activity was purified from P. berghei but was not attributed to any specific gene.\",\n      \"evidence\": \"Biochemical purification from P. berghei-infected erythrocytes with relaxation/unknotting/decatenation/catenation and drug inhibition assays\",\n      \"pmids\": [\"3011062\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"The purified subunits were not mapped to TOP6B at the gene level, so this activity cannot be assigned to PF3D7_1365600\",\n        \"Performed in P. berghei, not P. falciparum\",\n        \"No molecular identity of the ~160 kDa subunits established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether TOP6B contributes catalytically or structurally within the heterodimer, its atomic structure, and its role in parasite replication in vivo remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of TOP6B or the TOP6B–TOP6A complex\",\n        \"No in vitro reconstitution with fully purified recombinant subunits\",\n        \"No genetic dissection of TOP6B function during the P. falciparum life cycle\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003918\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005524\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0042803\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0000287\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006265\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"Type II topoisomerase VI (TOP6B–TOP6A heterodimer)\",\n      \"TOP6B homodimer\"\n    ],\n    \"partners\": [\n      \"TOP6A (PfTopoVIA, A subunit)\"\n    ],\n    \"other_free_text\": [\n      \"Decatenation activity of the TOP6B–TOP6A complex is inhibited by radicicol and etoposide but not by novobiocin [#0]\",\n      \"TOP6B alone cannot complement yeast ΔtopoII lethality; both TOP6B and TOP6A are required for activity [#0]\",\n      \"A native two-subunit, ATP/Mg2+-dependent topoisomerase II activity was purified from P. berghei but not assigned to PF3D7_1365600 at the gene level [#1]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1365600","name":null,"product":"DNA topoisomerase 6 subunit B","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1141400","name":null,"product":"DNA topoisomerase 6 subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1105700","name":null,"product":"DNA topoisomerase 6 subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"TOP6B","evaluation":null}