{"gene":"PF3D7_0628800","run_date":"2026-09-08T12:51:26","timeline":{"discoveries":[{"year":2015,"finding":"GATB (PF3D7_0628800) forms a unique heterodimeric glutamyl-tRNA amidotransferase complex (GatAB) together with GatA in P. falciparum; recombinant GatAB converts Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro, establishing the enzymatic activity of this complex in the indirect aminoacylation pathway.","method":"Recombinant protein expression and in vitro amidotransferase assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic reconstitution with recombinant protein, single lab but two orthogonal methods (biochemical assay + localization)","pmids":["26318454"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"GATB (PF3D7_0628800) localizes to the apicoplast in blood stage P. falciparum parasites, as demonstrated by direct localization experiments.","method":"Subcellular localization (fluorescence microscopy/fractionation)","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization experiment, single lab, single method","pmids":["26318454"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"The GatAB complex (including GATB/PF3D7_0628800) is essential for blood stage parasites: the P. berghei gene encoding the GatA subunit could not be deleted in blood stage parasites in vivo, indicating the entire complex is required for erythrocytic stage survival.","method":"Gene knockout attempt (failed deletion = essential gene) in P. berghei blood stage parasites in vivo","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic essentiality demonstrated by failed knockout, single lab, single method; finding attributed to GatA deletion but implies GATB-containing complex is essential","pmids":["26318454"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"GATB (PF3D7_0628800) is the B subunit of a unique heterodimeric glutamyl-tRNA amidotransferase (GatAB) that localizes to the P. falciparum apicoplast and catalyzes the conversion of mischarged Glu-tRNA(Gln) to Gln-tRNA(Gln) as part of the indirect aminoacylation pathway, a function essential for blood stage parasite survival."},"narrative":{"mechanistic_narrative":"GATB (PF3D7_0628800) is the B subunit of a unique heterodimeric glutamyl-tRNA amidotransferase (GatAB) in Plasmodium falciparum, functioning in the indirect aminoacylation pathway that generates correctly charged Gln-tRNA(Gln) [PMID:26318454]. Recombinant GatAB, formed by GATB together with the GatA subunit, converts mischarged Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro, establishing the transamidation activity of the complex [PMID:26318454]. GATB localizes to the apicoplast in blood-stage parasites, placing this activity within the organellar translation machinery [PMID:26318454]. Genetic evidence that the GatA subunit of the complex cannot be deleted in P. berghei blood-stage parasites indicates the GatAB complex is essential for erythrocytic-stage survival [PMID:26318454]. Beyond its role as the B subunit of this heterodimeric amidotransferase, no further GATB-specific mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2015,"claim":"Whether P. falciparum uses an indirect route to produce Gln-tRNA(Gln) and which enzyme performs the transamidation was unknown; reconstitution established that GATB, as part of the heterodimeric GatAB complex, catalyzes conversion of Glu-tRNA(Gln) to Gln-tRNA(Gln).","evidence":"Recombinant protein expression and in vitro amidotransferase assay","pmids":["26318454"],"confidence":"High","gaps":["The specific catalytic contribution of the GATB subunit versus GatA within the complex is not dissected","No structural model of the GATB-GatA heterodimer","Substrate/tRNA recognition determinants attributable to GATB not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"The subcellular compartment in which GATB acts was unknown; localization placed GATB in the apicoplast, tying its amidotransferase activity to organellar translation in blood-stage parasites.","evidence":"Subcellular localization by fluorescence microscopy/fractionation","pmids":["26318454"],"confidence":"Medium","gaps":["Single method, single lab localization","Import/targeting mechanism of GATB to the apicoplast not addressed","Localization across other life-cycle stages not examined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Whether the GatAB pathway is dispensable was unknown; failure to delete the GatA subunit indicated the complex is required for erythrocytic-stage survival.","evidence":"Failed gene knockout of the GatA subunit in P. berghei blood-stage parasites in vivo","pmids":["26318454"],"confidence":"Medium","gaps":["Essentiality was demonstrated via GatA, not by direct deletion of GATB itself","Conditional knockdown to confirm GATB-specific essentiality not performed","Requirement in non-blood stages not tested"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The GATB-specific catalytic mechanism, structural organization within GatAB, and direct genetic essentiality of GATB itself remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct GATB knockout or knockdown reported","No structural characterization of GATB","Regulation and stage-specific function unknown"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Glutamyl-tRNA(Gln) amidotransferase GatAB heterodimer (GATB + GatA)"],"partners":["GATA SUBUNIT"],"other_free_text":["GatAB complex is essential for P. falciparum/P. berghei blood-stage survival, inferred from failed deletion of the GatA subunit [#2]","Corpus establishes GATB primarily as the B subunit of the GatAB amidotransferase; no GATB-specific function outside this complex is characterized"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"26318454","id":"PMC_26318454","title":"Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26318454","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["GATB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3406,"output_tokens":840,"usd":0.011409,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5515,"output_tokens":1762,"usd":0.035812,"stage2_stop_reason":"end_turn"},"total_usd":0.047221,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"GATB (PF3D7_0628800) forms a unique heterodimeric glutamyl-tRNA amidotransferase complex (GatAB) together with GatA in P. falciparum; recombinant GatAB converts Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro, establishing the enzymatic activity of this complex in the indirect aminoacylation pathway.\",\n      \"method\": \"Recombinant protein expression and in vitro amidotransferase assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic reconstitution with recombinant protein, single lab but two orthogonal methods (biochemical assay + localization)\",\n      \"pmids\": [\"26318454\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"GATB (PF3D7_0628800) localizes to the apicoplast in blood stage P. falciparum parasites, as demonstrated by direct localization experiments.\",\n      \"method\": \"Subcellular localization (fluorescence microscopy/fractionation)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization experiment, single lab, single method\",\n      \"pmids\": [\"26318454\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The GatAB complex (including GATB/PF3D7_0628800) is essential for blood stage parasites: the P. berghei gene encoding the GatA subunit could not be deleted in blood stage parasites in vivo, indicating the entire complex is required for erythrocytic stage survival.\",\n      \"method\": \"Gene knockout attempt (failed deletion = essential gene) in P. berghei blood stage parasites in vivo\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic essentiality demonstrated by failed knockout, single lab, single method; finding attributed to GatA deletion but implies GATB-containing complex is essential\",\n      \"pmids\": [\"26318454\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"GATB (PF3D7_0628800) is the B subunit of a unique heterodimeric glutamyl-tRNA amidotransferase (GatAB) that localizes to the P. falciparum apicoplast and catalyzes the conversion of mischarged Glu-tRNA(Gln) to Gln-tRNA(Gln) as part of the indirect aminoacylation pathway, a function essential for blood stage parasite survival.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"GATB (PF3D7_0628800) is the B subunit of a unique heterodimeric glutamyl-tRNA amidotransferase (GatAB) in Plasmodium falciparum, functioning in the indirect aminoacylation pathway that generates correctly charged Gln-tRNA(Gln) [#0]. Recombinant GatAB, formed by GATB together with the GatA subunit, converts mischarged Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro, establishing the transamidation activity of the complex [#0]. GATB localizes to the apicoplast in blood-stage parasites, placing this activity within the organellar translation machinery [#1]. Genetic evidence that the GatA subunit of the complex cannot be deleted in P. berghei blood-stage parasites indicates the GatAB complex is essential for erythrocytic-stage survival [#2]. Beyond its role as the B subunit of this heterodimeric amidotransferase, no further GATB-specific mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether P. falciparum uses an indirect route to produce Gln-tRNA(Gln) and which enzyme performs the transamidation was unknown; reconstitution established that GATB, as part of the heterodimeric GatAB complex, catalyzes conversion of Glu-tRNA(Gln) to Gln-tRNA(Gln).\",\n      \"evidence\": \"Recombinant protein expression and in vitro amidotransferase assay\",\n      \"pmids\": [\"26318454\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The specific catalytic contribution of the GATB subunit versus GatA within the complex is not dissected\",\n        \"No structural model of the GATB-GatA heterodimer\",\n        \"Substrate/tRNA recognition determinants attributable to GATB not defined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The subcellular compartment in which GATB acts was unknown; localization placed GATB in the apicoplast, tying its amidotransferase activity to organellar translation in blood-stage parasites.\",\n      \"evidence\": \"Subcellular localization by fluorescence microscopy/fractionation\",\n      \"pmids\": [\"26318454\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single method, single lab localization\",\n        \"Import/targeting mechanism of GATB to the apicoplast not addressed\",\n        \"Localization across other life-cycle stages not examined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether the GatAB pathway is dispensable was unknown; failure to delete the GatA subunit indicated the complex is required for erythrocytic-stage survival.\",\n      \"evidence\": \"Failed gene knockout of the GatA subunit in P. berghei blood-stage parasites in vivo\",\n      \"pmids\": [\"26318454\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Essentiality was demonstrated via GatA, not by direct deletion of GATB itself\",\n        \"Conditional knockdown to confirm GATB-specific essentiality not performed\",\n        \"Requirement in non-blood stages not tested\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The GATB-specific catalytic mechanism, structural organization within GatAB, and direct genetic essentiality of GATB itself remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct GATB knockout or knockdown reported\",\n        \"No structural characterization of GATB\",\n        \"Regulation and stage-specific function unknown\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0050567\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0020011\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0070681\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"Glutamyl-tRNA(Gln) amidotransferase GatAB heterodimer (GATB + GatA)\"\n    ],\n    \"partners\": [\n      \"GatA subunit\"\n    ],\n    \"other_free_text\": [\n      \"GatAB complex is essential for P. falciparum/P. berghei blood-stage survival, inferred from failed deletion of the GatA subunit [#2]\",\n      \"Corpus establishes GATB primarily as the B subunit of the GatAB amidotransferase; no GATB-specific function outside this complex is characterized\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0628800","name":null,"product":"glutamyl-tRNA(Gln) amidotransferase subunit B","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1127500","name":null,"product":"glutamyl-tRNA(Gln) amidotransferase subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1121000","name":null,"product":"glutamyl-tRNA(Gln) amidotransferase subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"GATB","evaluation":null}