{"gene":"PBANKA_API00120","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2003,"finding":"sufB (encoded on the apicoplast genome of malaria parasites) physically interacts with SufC (ycf16, a nuclear-encoded ATPase imported into the plastid), as demonstrated by experimental evidence of a physical interaction between the two proteins.","method":"Physical interaction assay (pulldown/co-elution) between SufB and SufC","journal":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single interaction experiment reported in a review-style paper, but replicated in a subsequent independent study (PMID:21722645)","pmids":["12594924"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2011,"finding":"Apicoplast-encoded sufB (PfSufB) interacts with nuclear-encoded PfSufC in vitro; an internal region of PfSufB was sufficient for this interaction, and co-elution of SufB from parasite lysate with recombinant PfSufC on an affinity column confirmed the interaction in a parasite context. Unlike bacterial SufB, PfSufB exhibited ATPase activity, suggesting acquisition of a specialized function in the plastid counterpart.","method":"In vitro interaction assay using recombinant proteins; affinity column co-elution from parasite lysate; ATPase activity assay of recombinant PfSufB","journal":"International journal for parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal pulldown (recombinant + lysate co-elution) plus biochemical ATPase activity assay, two orthogonal methods, single lab","pmids":["21722645"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"finding":"Apicoplast-encoded PfSufB forms a complex with nuclear-encoded PfSufC and PfSufD (PfSufBC2D), as shown by in vitro interaction experiments and in vivo cross-linking; this PfSufBC2D complex functions as a scaffold that can assemble [4Fe-4S] clusters in vitro.","method":"In vitro protein interaction assays; in vivo chemical cross-linking; in vitro [4Fe-4S] cluster assembly assay","journal":"The FEBS journal","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (in vitro interaction, in vivo cross-linking, reconstituted in vitro cluster assembly), single lab with rigorous biochemical characterization","pmids":["28695709"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"In Plasmodium vivax, SufB is predicted to serve as a scaffold protein in conjunction with SufA for pre-assembly of Fe-S clusters; H-bond interactions at the PvSufA-SufB interface were modeled, and co-localization of SufA to the apicoplast was confirmed experimentally, consistent with sufB functioning in apicoplast Fe-S cluster biogenesis.","method":"Computational structural modeling of SufA-SufB interface; apicoplast co-localization of SufA by fluorescence microscopy","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 4 / Weak — interface modeling is computational; direct experimental evidence for sufB's scaffold role in P. vivax is not provided; localization data are for SufA, not sufB itself","pmids":["27033210"],"is_preprint":false,"attribution":[{"species":"Plasmodium vivax","strain":""}]}],"current_model":"sufB (PBANKA_API00120) encodes an apicoplast-genome-encoded protein that physically interacts with the nuclear-encoded ATPase SufC (and also SufD), forming a SufBC2D scaffold complex in the apicoplast of Plasmodium that assembles [4Fe-4S] clusters in vitro; unlike its bacterial counterpart, apicoplast SufB itself also exhibits ATPase activity, indicating functional specialization of the plastid Suf pathway."},"narrative":{"mechanistic_narrative":"sufB (PBANKA_API00120) is an apicoplast-genome-encoded component of the plastid SUF pathway for [Fe-S] cluster biogenesis in malaria parasites [PMID:12594924, PMID:28695709]. In Plasmodium falciparum, the sufB product physically interacts with the nuclear-encoded, apicoplast-imported ATPase SufC, an interaction demonstrated both between recombinant proteins and by co-elution of native SufB from parasite lysate, with an internal region of SufB sufficient for binding [PMID:12594924, PMID:21722645]. SufB additionally associates with SufD, and the three proteins assemble into a SufBC2D complex that functions as a scaffold capable of assembling [4Fe-4S] clusters in vitro, as shown by reconstituted cluster-assembly assays and in vivo cross-linking [PMID:28695709]. Distinct from its bacterial counterpart, P. falciparum SufB itself exhibits ATPase activity, indicating functional specialization of the plastid Suf machinery [PMID:21722645]. Beyond its role as a scaffold subunit within this apicoplast complex, no further mechanistic detail specific to PBANKA_API00120 has been characterized in the available corpus.","teleology":[{"year":2003,"claim":"Establishing whether the apicoplast-encoded sufB protein has a functional partner addressed whether malaria parasites operate a plastid SUF pathway that bridges genomes; the finding showed sufB physically engages a nuclear-encoded partner.","evidence":"Physical interaction assay between apicoplast-encoded SufB and nuclear-encoded SufC (ycf16) in Plasmodium falciparum","pmids":["12594924"],"confidence":"Medium","gaps":["Single interaction experiment reported in a review-style paper without stoichiometry or interface mapping","No functional consequence of the interaction demonstrated","No cluster-assembly activity tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2011,"claim":"It was unknown whether the SufB-SufC interaction occurred in a parasite context and whether SufB carried enzymatic activity; reciprocal pulldowns plus a biochemical assay confirmed the interaction and revealed that Plasmodium SufB, unlike bacterial SufB, has ATPase activity.","evidence":"In vitro interaction with recombinant proteins, affinity co-elution of SufB from P. falciparum lysate, and ATPase activity assay of recombinant PfSufB","pmids":["21722645"],"confidence":"Medium","gaps":["The interaction-sufficient internal region of SufB was not resolved structurally","Physiological relevance of SufB ATPase activity to cluster assembly not established","Single-lab characterization"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"claim":"Whether SufB pairs with additional scaffold factors was probed in a second species; modeling and localization data placed SufB alongside SufA in apicoplast Fe-S pre-assembly, though the direct evidence concerned SufA rather than SufB itself.","evidence":"Computational modeling of the SufA-SufB interface and fluorescence-microscopy apicoplast localization of SufA in Plasmodium vivax","pmids":["27033210"],"confidence":"Low","gaps":["Interface prediction is computational with no experimental validation of the P. vivax SufA-SufB contact","Localization data are for SufA, not sufB itself","No direct demonstration of sufB scaffold function in P. vivax"],"attribution":[{"species":"Plasmodium vivax","strain":""}]},{"year":2017,"claim":"It was unresolved whether SufB-containing assemblies could actually build metal clusters; reconstitution showed SufB forms a SufBC2D complex that acts as a functional scaffold assembling [4Fe-4S] clusters in vitro.","evidence":"In vitro protein interaction assays, in vivo chemical cross-linking, and reconstituted [4Fe-4S] cluster assembly assay in Plasmodium falciparum","pmids":["28695709"],"confidence":"High","gaps":["Cluster-transfer to downstream apoprotein acceptors not demonstrated","Stoichiometry and structural architecture of SufBC2D not resolved","In vivo requirement of sufB for parasite viability not tested via genetics in this study"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PBANKA_API00120 (the Plasmodium berghei sufB ortholog itself) is essential and how the SufBC2D scaffold transfers assembled [4Fe-4S] clusters to downstream apicoplast acceptors remains unestablished in the available corpus.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct functional or genetic data on the P. berghei gene itself; all mechanistic evidence derives from P. falciparum and P. vivax orthologs","Downstream cluster-recipient proteins not identified","Structural model of the assembled complex absent"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["SufBC2D scaffold complex (SufB-SufC2-SufD)"],"partners":["SUFC (NUCLEAR-ENCODED, APICOPLAST-IMPORTED ATPASE)","SUFD","SUFA (P. VIVAX, PREDICTED INTERFACE)"],"other_free_text":["sufB is encoded on the apicoplast genome, while its partner SufC is nuclear-encoded and imported into the plastid [#0, #1].","Unlike bacterial SufB, Plasmodium falciparum SufB displays intrinsic ATPase activity [#1].","The SufBC2D complex reconstitutes [4Fe-4S] cluster assembly in vitro [#2].","All direct evidence derives from P. falciparum and P. vivax orthologs; no P. berghei-specific functional data for PBANKA_API00120 are present in the corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"11555280","id":"PMC_11555280","title":"Nifs and Sufs in malaria.","date":"2001","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/11555280","citation_count":80,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["sufB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21722645","id":"PMC_21722645","title":"Interaction between sulphur mobilisation proteins SufB and SufC: evidence for an iron-sulphur cluster biogenesis pathway in the apicoplast of Plasmodium falciparum.","date":"2011","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/21722645","citation_count":39,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["sufB","PfsufB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28695709","id":"PMC_28695709","title":"[Fe-S] cluster assembly in the apicoplast and its indispensability in mosquito stages of the malaria parasite.","date":"2017","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/28695709","citation_count":30,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["PfsufB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"12594924","id":"PMC_12594924","title":"Parasite plastids: maintenance and functions.","date":"2003","source":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/12594924","citation_count":25,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["sufB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27033210","id":"PMC_27033210","title":"Structural and functional characterization of an iron-sulfur cluster assembly scaffold protein-SufA from Plasmodium vivax.","date":"2016","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/27033210","citation_count":11,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["sufB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22266119","id":"PMC_22266119","title":"Plasmodium vivax apicoplast genome: a comparative analysis of major genes from Indian field isolates.","date":"2012","source":"Acta tropica","url":"https://pubmed.ncbi.nlm.nih.gov/22266119","citation_count":10,"is_preprint":false,"source_species":["Pb"],"role":"primary","match_terms":["sufB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5482,"output_tokens":1224,"usd":0.017403,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6104,"output_tokens":2608,"usd":0.04786,"stage2_stop_reason":"end_turn"},"total_usd":0.065263,"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\": 2003,\n      \"finding\": \"sufB (encoded on the apicoplast genome of malaria parasites) physically interacts with SufC (ycf16, a nuclear-encoded ATPase imported into the plastid), as demonstrated by experimental evidence of a physical interaction between the two proteins.\",\n      \"method\": \"Physical interaction assay (pulldown/co-elution) between SufB and SufC\",\n      \"journal\": \"Philosophical transactions of the Royal Society of London. Series B, Biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single interaction experiment reported in a review-style paper, but replicated in a subsequent independent study (PMID:21722645)\",\n      \"pmids\": [\"12594924\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Apicoplast-encoded sufB (PfSufB) interacts with nuclear-encoded PfSufC in vitro; an internal region of PfSufB was sufficient for this interaction, and co-elution of SufB from parasite lysate with recombinant PfSufC on an affinity column confirmed the interaction in a parasite context. Unlike bacterial SufB, PfSufB exhibited ATPase activity, suggesting acquisition of a specialized function in the plastid counterpart.\",\n      \"method\": \"In vitro interaction assay using recombinant proteins; affinity column co-elution from parasite lysate; ATPase activity assay of recombinant PfSufB\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal pulldown (recombinant + lysate co-elution) plus biochemical ATPase activity assay, two orthogonal methods, single lab\",\n      \"pmids\": [\"21722645\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Apicoplast-encoded PfSufB forms a complex with nuclear-encoded PfSufC and PfSufD (PfSufBC2D), as shown by in vitro interaction experiments and in vivo cross-linking; this PfSufBC2D complex functions as a scaffold that can assemble [4Fe-4S] clusters in vitro.\",\n      \"method\": \"In vitro protein interaction assays; in vivo chemical cross-linking; in vitro [4Fe-4S] cluster assembly assay\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (in vitro interaction, in vivo cross-linking, reconstituted in vitro cluster assembly), single lab with rigorous biochemical characterization\",\n      \"pmids\": [\"28695709\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In Plasmodium vivax, SufB is predicted to serve as a scaffold protein in conjunction with SufA for pre-assembly of Fe-S clusters; H-bond interactions at the PvSufA-SufB interface were modeled, and co-localization of SufA to the apicoplast was confirmed experimentally, consistent with sufB functioning in apicoplast Fe-S cluster biogenesis.\",\n      \"method\": \"Computational structural modeling of SufA-SufB interface; apicoplast co-localization of SufA by fluorescence microscopy\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — interface modeling is computational; direct experimental evidence for sufB's scaffold role in P. vivax is not provided; localization data are for SufA, not sufB itself\",\n      \"pmids\": [\"27033210\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium vivax\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"sufB (PBANKA_API00120) encodes an apicoplast-genome-encoded protein that physically interacts with the nuclear-encoded ATPase SufC (and also SufD), forming a SufBC2D scaffold complex in the apicoplast of Plasmodium that assembles [4Fe-4S] clusters in vitro; unlike its bacterial counterpart, apicoplast SufB itself also exhibits ATPase activity, indicating functional specialization of the plastid Suf pathway.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"sufB (PBANKA_API00120) is an apicoplast-genome-encoded component of the plastid SUF pathway for [Fe-S] cluster biogenesis in malaria parasites [#0, #2]. In Plasmodium falciparum, the sufB product physically interacts with the nuclear-encoded, apicoplast-imported ATPase SufC, an interaction demonstrated both between recombinant proteins and by co-elution of native SufB from parasite lysate, with an internal region of SufB sufficient for binding [#0, #1]. SufB additionally associates with SufD, and the three proteins assemble into a SufBC2D complex that functions as a scaffold capable of assembling [4Fe-4S] clusters in vitro, as shown by reconstituted cluster-assembly assays and in vivo cross-linking [#2]. Distinct from its bacterial counterpart, P. falciparum SufB itself exhibits ATPase activity, indicating functional specialization of the plastid Suf machinery [#1]. Beyond its role as a scaffold subunit within this apicoplast complex, no further mechanistic detail specific to PBANKA_API00120 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Establishing whether the apicoplast-encoded sufB protein has a functional partner addressed whether malaria parasites operate a plastid SUF pathway that bridges genomes; the finding showed sufB physically engages a nuclear-encoded partner.\",\n      \"evidence\": \"Physical interaction assay between apicoplast-encoded SufB and nuclear-encoded SufC (ycf16) in Plasmodium falciparum\",\n      \"pmids\": [\"12594924\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Single interaction experiment reported in a review-style paper without stoichiometry or interface mapping\",\n        \"No functional consequence of the interaction demonstrated\",\n        \"No cluster-assembly activity tested\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"It was unknown whether the SufB-SufC interaction occurred in a parasite context and whether SufB carried enzymatic activity; reciprocal pulldowns plus a biochemical assay confirmed the interaction and revealed that Plasmodium SufB, unlike bacterial SufB, has ATPase activity.\",\n      \"evidence\": \"In vitro interaction with recombinant proteins, affinity co-elution of SufB from P. falciparum lysate, and ATPase activity assay of recombinant PfSufB\",\n      \"pmids\": [\"21722645\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"The interaction-sufficient internal region of SufB was not resolved structurally\",\n        \"Physiological relevance of SufB ATPase activity to cluster assembly not established\",\n        \"Single-lab characterization\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Whether SufB pairs with additional scaffold factors was probed in a second species; modeling and localization data placed SufB alongside SufA in apicoplast Fe-S pre-assembly, though the direct evidence concerned SufA rather than SufB itself.\",\n      \"evidence\": \"Computational modeling of the SufA-SufB interface and fluorescence-microscopy apicoplast localization of SufA in Plasmodium vivax\",\n      \"pmids\": [\"27033210\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Interface prediction is computational with no experimental validation of the P. vivax SufA-SufB contact\",\n        \"Localization data are for SufA, not sufB itself\",\n        \"No direct demonstration of sufB scaffold function in P. vivax\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium vivax\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"It was unresolved whether SufB-containing assemblies could actually build metal clusters; reconstitution showed SufB forms a SufBC2D complex that acts as a functional scaffold assembling [4Fe-4S] clusters in vitro.\",\n      \"evidence\": \"In vitro protein interaction assays, in vivo chemical cross-linking, and reconstituted [4Fe-4S] cluster assembly assay in Plasmodium falciparum\",\n      \"pmids\": [\"28695709\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Cluster-transfer to downstream apoprotein acceptors not demonstrated\",\n        \"Stoichiometry and structural architecture of SufBC2D not resolved\",\n        \"In vivo requirement of sufB for parasite viability not tested via genetics in this study\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PBANKA_API00120 (the Plasmodium berghei sufB ortholog itself) is essential and how the SufBC2D scaffold transfers assembled [4Fe-4S] clusters to downstream apicoplast acceptors remains unestablished in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No direct functional or genetic data on the P. berghei gene itself; all mechanistic evidence derives from P. falciparum and P. vivax orthologs\",\n        \"Downstream cluster-recipient proteins not identified\",\n        \"Structural model of the assembled complex absent\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016887\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0016226\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0051536\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0020011\", \"supporting_discovery_ids\": [0, 1, 2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016226\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [\n      \"SufBC2D scaffold complex (SufB-SufC2-SufD)\"\n    ],\n    \"partners\": [\n      \"SufC (nuclear-encoded, apicoplast-imported ATPase)\",\n      \"SufD\",\n      \"SufA (P. vivax, predicted interface)\"\n    ],\n    \"other_free_text\": [\n      \"sufB is encoded on the apicoplast genome, while its partner SufC is nuclear-encoded and imported into the plastid [#0, #1].\",\n      \"Unlike bacterial SufB, Plasmodium falciparum SufB displays intrinsic ATPase activity [#1].\",\n      \"The SufBC2D complex reconstitutes [4Fe-4S] cluster assembly in vitro [#2].\",\n      \"All direct evidence derives from P. falciparum and P. vivax orthologs; no P. berghei-specific functional data for PBANKA_API00120 are present in the corpus.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"PbANKA","gene_id":"PBANKA_API00120","name":null,"product":"iron-sulfur cluster assembly protein SufB, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"sufB","evaluation":null}