{"gene":"PF3D7_1111100","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2010,"finding":"RFC5 (PfRFC-5) was identified as a physical interactor of the malarial CDK Pfmrk via bacterial two-hybrid screen of a P. falciparum cDNA library, and was demonstrated to be a substrate of Pfmrk-mediated phosphorylation; PfMAT1 (the Pfmrk activator) confers substrate specificity to the Pfmrk kinase complex for this phosphorylation.","method":"Bacterial two-hybrid screen (interaction identification); in vitro kinase assay (phosphorylation of PfRFC-5 by Pfmrk); co-immunoprecipitation (Pfmrk–PfMAT1 complex validation)","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — bacterial two-hybrid plus kinase assay in a single lab; direct interaction between RFC5 and Pfmrk was not confirmed by reciprocal Co-IP, and phosphorylation was demonstrated in a single study","pmids":["20332005"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"P. falciparum RFC5 (PF3D7_1111100), a putative subunit of the replication factor C clamp-loader complex, physically interacts with the malarial CDK Pfmrk and is phosphorylated by the Pfmrk–PfMAT1 kinase complex (with PfMAT1 conferring substrate specificity), suggesting that Pfmrk regulates the DNA replication machinery through phosphorylation of RFC5 in the parasite nucleus."},"narrative":{"mechanistic_narrative":"RFC5 (PF3D7_1111100) is a putative subunit of the replication factor C clamp-loader complex in Plasmodium falciparum that has been characterized in the available corpus only through its connection to the malarial CDK Pfmrk [PMID:20332005]. It was identified as a physical interactor of Pfmrk in a bacterial two-hybrid screen and is a substrate of Pfmrk-mediated phosphorylation, with the Pfmrk activator PfMAT1 conferring substrate specificity to the kinase complex for this reaction [PMID:20332005]. This links RFC5 to potential cell-cycle-dependent regulation of the parasite's DNA replication machinery. Beyond this interaction and phosphorylation relationship [PMID:20332005], no further mechanistic detail — including any direct demonstration of clamp-loader activity, DNA-binding, or subunit assembly for RFC5 itself — has been characterized in the available corpus.","teleology":[{"year":2010,"claim":"To connect the malarial CDK Pfmrk to a cellular process, an unbiased interactor search was needed; identifying RFC5 as a binding partner and phosphorylation substrate established a candidate link between Pfmrk signaling and the parasite DNA replication apparatus.","evidence":"Bacterial two-hybrid screen of a P. falciparum cDNA library, in vitro kinase assay, and co-immunoprecipitation validation of the Pfmrk–PfMAT1 complex","pmids":["20332005"],"confidence":"Medium","gaps":["Direct RFC5–Pfmrk interaction was not confirmed by reciprocal Co-IP","Phosphorylation was shown in vitro in a single study; in vivo phosphosite and functional consequence for RFC5 are undefined","No demonstration that RFC5 functions as a clamp-loader subunit or participates in DNA replication in the parasite"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether Pfmrk-mediated phosphorylation of RFC5 regulates its assembly into the replication factor C complex or its clamp-loading function during parasite DNA replication remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No functional assay of RFC5 clamp-loader activity","No structural or complex-assembly data for RFC5 in P. falciparum","Phenotypic consequence of RFC5 phosphorylation for parasite replication is unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["replication factor C complex (putative subunit)"],"partners":["PFMRK (MALARIAL CDK)","PFMAT1 (PFMRK ACTIVATOR, CONFERS SUBSTRATE SPECIFICITY)"],"other_free_text":["RFC5 (PF3D7_1111100) is a substrate of the Pfmrk–PfMAT1 kinase complex [#0].","Characterization in the available corpus is limited to a single study establishing interaction with and phosphorylation by Pfmrk; RFC5's own clamp-loader function has not been directly demonstrated."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"20332005","id":"PMC_20332005","title":"The malarial CDK Pfmrk and its effector PfMAT1 phosphorylate DNA replication proteins and co-localize in the nucleus.","date":"2010","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/20332005","citation_count":26,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRFC5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16082778","id":"","title":"Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases.","date":"2005","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/16082778","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RFC5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4464,"output_tokens":481,"usd":0.010304,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5015,"output_tokens":1318,"usd":0.029013,"stage2_stop_reason":"end_turn"},"total_usd":0.039317,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"RFC5 (PfRFC-5) was identified as a physical interactor of the malarial CDK Pfmrk via bacterial two-hybrid screen of a P. falciparum cDNA library, and was demonstrated to be a substrate of Pfmrk-mediated phosphorylation; PfMAT1 (the Pfmrk activator) confers substrate specificity to the Pfmrk kinase complex for this phosphorylation.\",\n      \"method\": \"Bacterial two-hybrid screen (interaction identification); in vitro kinase assay (phosphorylation of PfRFC-5 by Pfmrk); co-immunoprecipitation (Pfmrk–PfMAT1 complex validation)\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — bacterial two-hybrid plus kinase assay in a single lab; direct interaction between RFC5 and Pfmrk was not confirmed by reciprocal Co-IP, and phosphorylation was demonstrated in a single study\",\n      \"pmids\": [\"20332005\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"P. falciparum RFC5 (PF3D7_1111100), a putative subunit of the replication factor C clamp-loader complex, physically interacts with the malarial CDK Pfmrk and is phosphorylated by the Pfmrk–PfMAT1 kinase complex (with PfMAT1 conferring substrate specificity), suggesting that Pfmrk regulates the DNA replication machinery through phosphorylation of RFC5 in the parasite nucleus.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RFC5 (PF3D7_1111100) is a putative subunit of the replication factor C clamp-loader complex in Plasmodium falciparum that has been characterized in the available corpus only through its connection to the malarial CDK Pfmrk [#0]. It was identified as a physical interactor of Pfmrk in a bacterial two-hybrid screen and is a substrate of Pfmrk-mediated phosphorylation, with the Pfmrk activator PfMAT1 conferring substrate specificity to the kinase complex for this reaction [#0]. This links RFC5 to potential cell-cycle-dependent regulation of the parasite's DNA replication machinery. Beyond this interaction and phosphorylation relationship [#0], no further mechanistic detail — including any direct demonstration of clamp-loader activity, DNA-binding, or subunit assembly for RFC5 itself — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"To connect the malarial CDK Pfmrk to a cellular process, an unbiased interactor search was needed; identifying RFC5 as a binding partner and phosphorylation substrate established a candidate link between Pfmrk signaling and the parasite DNA replication apparatus.\",\n      \"evidence\": \"Bacterial two-hybrid screen of a P. falciparum cDNA library, in vitro kinase assay, and co-immunoprecipitation validation of the Pfmrk–PfMAT1 complex\",\n      \"pmids\": [\"20332005\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct RFC5–Pfmrk interaction was not confirmed by reciprocal Co-IP\",\n        \"Phosphorylation was shown in vitro in a single study; in vivo phosphosite and functional consequence for RFC5 are undefined\",\n        \"No demonstration that RFC5 functions as a clamp-loader subunit or participates in DNA replication in the parasite\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether Pfmrk-mediated phosphorylation of RFC5 regulates its assembly into the replication factor C complex or its clamp-loading function during parasite DNA replication remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional assay of RFC5 clamp-loader activity\",\n        \"No structural or complex-assembly data for RFC5 in P. falciparum\",\n        \"Phenotypic consequence of RFC5 phosphorylation for parasite replication is unknown\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0019901\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006260\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"replication factor C complex (putative subunit)\"\n    ],\n    \"partners\": [\n      \"Pfmrk (malarial CDK)\",\n      \"PfMAT1 (Pfmrk activator, confers substrate specificity)\"\n    ],\n    \"other_free_text\": [\n      \"RFC5 (PF3D7_1111100) is a substrate of the Pfmrk–PfMAT1 kinase complex [#0].\",\n      \"Characterization in the available corpus is limited to a single study establishing interaction with and phosphorylation by Pfmrk; RFC5's own clamp-loader function has not been directly demonstrated.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1111100","name":null,"product":"replication factor C subunit 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0936500","name":null,"product":"replication factor C subunit 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0908800","name":null,"product":"replication factor C subunit 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RFC5","evaluation":null}