{"gene":"PF3D7_0922900","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2006,"finding":"PfFabG (3-oxoacyl-ACP reductase) was crystallized at 1.5 Å resolution, revealing a homotetrameric structure with a catalytic triad of serine, tyrosine, and lysine aligned in an active conformation; a sulphate ion occupies the cofactor-binding site; and a cluster of positively charged residues at the active-site entrance is consistent with ACP substrate recognition. Kinetic and product inhibition studies indicated a steady-state ordered mechanism, with NADPH binding to the free enzyme first. Activity with NADH was <3% of that with NADPH. Hexachlorophene inhibited FabG with IC50 2.05 µM via non-linear competitive inhibition with respect to NADPH.","method":"X-ray crystallography (1.5 Å), fluorescence enhancement binding assays, kinetic analysis (steady-state ordered mechanism), product inhibition, in vitro enzymatic assay, inhibitor titration","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation by kinetic and inhibition assays, multiple orthogonal methods in a single rigorous study","pmids":["16225460"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2003,"finding":"Recombinant P. falciparum FabG expressed in E. coli is soluble and enzymatically active, catalyzing reduction of acetoacetyl-CoA with Km 75 µM, Vmax 0.0054 µmol/min/ml, and kcat 0.014 s−1. NADPH exhibits negative cooperativity in binding to FabG. Homology modeling using Brassica napus FabG as template provided a structural rationale for NADPH cofactor specificity.","method":"Recombinant protein expression in E. coli, in vitro enzymatic assay with acetoacetyl-CoA, kinetic characterization, homology modeling","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with kinetic characterization and homology modeling, single lab","pmids":["12646215"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"finding":"Binding of NADPH to PfFabG increases the binding affinity of substrate acetoacetyl-CoA by 16-fold and increases affinity for acyl carrier protein (ACP) approximately 3-fold, demonstrating ordered cofactor-mediated activation. PfFabG exhibits negative homotropic cooperativity for NADPH, which is enhanced in the presence of ACP. ACP increases NADPH accessibility to PfFabG. In the presence of NADP+, the reverse reaction is also observed (Ka = 23.17 µM−1).","method":"Intrinsic fluorescence spectroscopy (Trp334 nm), NADPH fluorescence (450 nm), acrylamide quenching assays, binding affinity measurements","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple fluorescence-based binding assays, single lab, two orthogonal readouts","pmids":["16934037"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"Arg187 and Arg230 of PfFabG are critical residues for interaction with P. falciparum ACP (PfACP). Mutagenesis of Arg187, Arg190, and Arg230 reduced affinities of PfFabG mutants for acetoacetyl-ACP (the physiological substrate) compared to wild-type, while activity with the substrate analog acetoacetyl-CoA was retained. Surface plasmon resonance and intrinsic fluorescence confirmed direct PfFabG–PfACP binding, identifying a positively charged/hydrophobic patch adjacent to the active site as the ACP interaction site.","method":"Site-directed mutagenesis, ACP-dependent and ACP-independent enzymatic assays, intrinsic fluorescence binding assays, surface plasmon resonance","journal":"The FEBS journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis combined with SPR and fluorescence binding assays and kinetic activity measurements, multiple orthogonal methods, single lab","pmids":["18721141"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"The elongation module of P. falciparum FAS-II was reconstituted in vitro using all four enzymes—FabB/F, FabG, FabZ, and FabI—and the reaction products were analyzed by MALDI-TOF MS. The distribution of acyl products from the reconstituted system matched the in vivo pattern, confirming FabG participates sequentially in iterative fatty acid chain elongation. Inhibition of FabG by (-)-catechin gallate led to accumulation of the upstream intermediate, detectable by MS.","method":"In vitro reconstitution of FAS-II elongation module, MALDI-TOF MS product analysis, inhibitor perturbation assay","journal":"Antimicrobial agents and chemotherapy","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with MS-based product analysis, inhibitor-intermediate accumulation confirms pathway position, single lab","pmids":["17485508"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"PfFabG is a homotetramer (Mr ~120,000) belonging to the short-chain alcohol dehydrogenase/reductase (SDR) superfamily. Guanidinium chloride-induced denaturation follows a simple A4 ↔ 4A two-state unfolding model. Conformational stability (ΔGs) is 22.68 kcal/mol with ΔCp of 5.83 kcal/(mol·K), attributed to the large tetrameric size and buried hydrophobic core.","method":"Intrinsic fluorescence spectroscopy, circular dichroism, denaturant-induced unfolding, enzymatic activity measurements, thermodynamic analysis","journal":"IUBMB life","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biophysical methods (fluorescence, CD, activity), two-state unfolding model validated by concentration independence, single lab","pmids":["17654120"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"Urea-induced unfolding of PfFabG is a multi-step process, whereas GdmCl-induced unfolding is two-state. In the presence of NADPH during urea unfolding, an activity-enhanced intermediate state is populated at ~1 M urea (90% activity recovered upon dilution), while NADPH provides no stabilization during GdmCl unfolding. NADPH binding leads to compaction of PfFabG structure as evidenced by decreased tryptophan accessibility to acrylamide quenching.","method":"Intrinsic fluorescence, circular dichroism, enzymatic activity measurement, glutaraldehyde cross-linking, size exclusion chromatography, acrylamide quenching","journal":"Proteins","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biophysical methods, single lab, cofactor-dependent conformational effect validated across assays","pmids":["17879351"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"finding":"Flavonoids inhibit PfFabG in a noncompetitive manner (luteolin and (-)-catechin gallate used as model compounds in kinetic analysis), establishing the mode of inhibition at the enzyme level. C-3 gallic acid esters of catechins are the most potent inhibitors (IC50 0.2–1.1 µM).","method":"In vitro enzyme inhibition assay, kinetic analysis (mode of inhibition determination), IC50 determination","journal":"Journal of medicinal chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — kinetic mode-of-inhibition analysis with defined compounds, single lab, inhibitor mechanism established","pmids":["16722653"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"PfFabG overexpressed in E. coli as inclusion bodies could be correctly refolded only in the presence of the cofactor NADPH and 300 mM NaCl, demonstrating that NADPH is required for proper folding of the recombinant enzyme. The refolded protein was enzymatically active with acetoacetyl-CoA.","method":"Recombinant protein expression, inclusion body refolding, enzymatic activity assay","journal":"Protein expression and purification","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single method (refolding/activity assay), cofactor-dependent folding is an indirect inference, single lab","pmids":["15939298"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PfFabG (PF3D7_0922900) is a homotetrameric NADPH-dependent 3-oxoacyl-ACP reductase of the SDR superfamily that catalyzes the first reductive step in the P. falciparum type II fatty acid biosynthesis elongation cycle via a steady-state ordered mechanism (NADPH binds first); NADPH binding compacts the protein and increases substrate (acetoacetyl-ACP) and ACP binding affinity by 16-fold and ~3-fold respectively; Arg187 and Arg230 in a positively charged patch adjacent to the active site mediate critical interactions with the acyl carrier protein (PfACP); and the enzyme has been positioned within the FAS-II elongation module by in vitro reconstitution, where its inhibition leads to detectable accumulation of upstream intermediates."},"narrative":{"mechanistic_narrative":"FabG (PF3D7_0922900) is the NADPH-dependent 3-oxoacyl-[acyl-carrier-protein] reductase that catalyzes the first reductive step of the iterative type II fatty acid biosynthesis (FAS-II) elongation cycle in Plasmodium falciparum [PMID:16225460, PMID:17485508]. It is a homotetramer of the short-chain dehydrogenase/reductase (SDR) superfamily with a Ser/Tyr/Lys catalytic triad and a marked preference for NADPH over NADH [PMID:16225460, PMID:17654120]. The enzyme operates by a steady-state ordered mechanism in which NADPH binds the free enzyme first; cofactor binding compacts the protein and increases affinity for the acetoacetyl-ACP substrate ~16-fold and for the acyl carrier protein PfACP ~3-fold, so that cofactor loading gates productive substrate engagement [PMID:16225460, PMID:16934037, PMID:17879351]. Recognition of the physiological ACP-tethered substrate occurs through a positively charged, hydrophobic patch adjacent to the active site, with Arg187 and Arg230 mediating critical direct contacts to PfACP [PMID:16225460, PMID:18721141]. Within a reconstituted FAS-II elongation module (FabB/F, FabG, FabZ, FabI), FabG acts sequentially in chain elongation, and its inhibition causes accumulation of the upstream intermediate, fixing its position in the pathway [PMID:17485508]. FabG is inhibited in vitro by hexachlorophene and by flavonoids, most potently C-3 gallic acid esters of catechins [PMID:16225460, PMID:16722653]. No genetic loss-of-function or in vivo parasite phenotype for FabG has been characterized in the available corpus.","teleology":[{"year":2003,"claim":"Establishing that the P. falciparum FabG gene product is a bona fide, soluble, catalytically active reductase was the first step in defining a candidate FAS-II enzyme; recombinant expression answered whether the annotated gene encodes a functional 3-oxoacyl reductase.","evidence":"recombinant expression in E. coli with in vitro kinetics on acetoacetyl-CoA and homology modeling","pmids":["12646215"],"confidence":"Medium","gaps":["kinetics measured on the CoA analog rather than the physiological ACP-linked substrate","no structural data to confirm the modeled NADPH specificity","cellular role in the parasite not addressed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"claim":"Refolding experiments probed the relationship between cofactor and enzyme integrity, showing NADPH is not merely catalytic but is required for correct folding of the recombinant enzyme.","evidence":"inclusion-body refolding restored only in the presence of NADPH and NaCl, with activity readout","pmids":["15939298"],"confidence":"Low","gaps":["cofactor-dependent folding is an indirect inference from a single refolding/activity assay","does not establish whether native in vivo folding requires NADPH","no structural characterization of the refolded species"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"claim":"The 1.5 Å crystal structure resolved the catalytic architecture and cofactor logic, answering how the enzyme is organized and why it prefers NADPH — defining the Ser/Tyr/Lys triad, the tetrameric assembly, and a steady-state ordered mechanism with NADPH binding first.","evidence":"X-ray crystallography with kinetic and product-inhibition analysis and inhibitor titration (hexachlorophene)","pmids":["16225460"],"confidence":"High","gaps":["cofactor site occupied by sulphate rather than NADPH, so cofactor-bound conformation inferred","no co-crystal with ACP or acyl substrate","ACP recognition inferred from surface charge, not directly visualized"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"claim":"Binding studies established the allosteric consequence of the ordered mechanism — that NADPH loading actively primes the enzyme for substrate and ACP engagement — explaining how cofactor order translates into catalytic control.","evidence":"intrinsic and NADPH fluorescence, acrylamide quenching, and affinity measurements","pmids":["16934037"],"confidence":"Medium","gaps":["negative cooperativity for NADPH not linked to a structural transition","physiological relevance of the observed reverse reaction unclear","single-lab fluorescence approach"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"claim":"Kinetic mode-of-inhibition analysis of flavonoids defined FabG as a druggable target and characterized how flavonoid inhibitors act, identifying noncompetitive inhibition and the most potent chemical class.","evidence":"in vitro enzyme inhibition kinetics and IC50 determination for catechin/flavonoid series","pmids":["16722653"],"confidence":"Medium","gaps":["inhibition characterized only in vitro, not in parasites","binding site of noncompetitive inhibitors not mapped","selectivity over host reductases not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"In vitro reconstitution of the full FAS-II elongation module placed FabG in the sequential elongation cycle, answering where in the pathway the enzyme acts by showing its inhibition stalls the cycle at an upstream intermediate.","evidence":"reconstitution of FabB/F, FabG, FabZ, FabI with MALDI-TOF product profiling and inhibitor perturbation","pmids":["17485508"],"confidence":"High","gaps":["pathway assembled in vitro rather than in the parasite","does not address regulation of the cycle in vivo","no genetic confirmation of FabG requirement"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"Biophysical characterization defined the enzyme's oligomeric state and stability, confirming a homotetrameric SDR-family protein with a two-state GdmCl unfolding transition.","evidence":"fluorescence, CD, denaturant unfolding, and thermodynamic analysis","pmids":["17654120"],"confidence":"Medium","gaps":["stability measured on recombinant protein only","does not connect fold stability to catalytic regulation","single-lab thermodynamic model"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"Unfolding studies with cofactor revealed that NADPH binding compacts the enzyme and populates an activity-enhanced intermediate, linking cofactor binding to a defined conformational change.","evidence":"urea vs GdmCl unfolding with CD, fluorescence, cross-linking, SEC and acrylamide quenching","pmids":["17879351"],"confidence":"Medium","gaps":["compaction inferred from indirect quenching/unfolding readouts","structural basis of the intermediate not resolved","physiological significance of the intermediate state unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"Mutagenesis identified the specific residues mediating recognition of the physiological ACP-tethered substrate, answering how FabG discriminates ACP-linked acetoacetyl from the free CoA analog — Arg187 and Arg230 form the PfACP interaction site.","evidence":"site-directed mutagenesis with ACP-dependent vs ACP-independent activity, SPR, and fluorescence binding","pmids":["18721141"],"confidence":"High","gaps":["ACP-bound complex not structurally resolved","mutant catalytic mechanism retained on CoA analog, so effect is on ACP docking only","no in vivo test of these residues"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The in vivo essentiality, genetic loss-of-function phenotype, and validation of FabG as an antimalarial drug target in the intact parasite remain unaddressed in the available corpus.","evidence":"","pmids":[],"confidence":"Low","gaps":["no gene knockout or conditional knockdown reported","no demonstration that inhibitors kill parasites via FabG","no structure of the FabG–PfACP or FabG–NADPH complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Homotetramer (FabG A4 assembly)","FAS-II elongation module (with FabB/F, FabZ, FabI; in vitro reconstitution)"],"partners":["PFACP (ACYL CARRIER PROTEIN; DIRECT BINDING VIA ARG187/ARG230)","NADPH (COFACTOR)"],"other_free_text":["SDR superfamily member with Ser/Tyr/Lys catalytic triad.","Steady-state ordered mechanism: NADPH binds free enzyme first; NADPH increases acetoacetyl-ACP affinity ~16-fold and ACP affinity ~3-fold.","Exhibits negative homotropic cooperativity for NADPH, enhanced by ACP.","NADPH binding compacts the protein and stabilizes an activity-enhanced intermediate.","Inhibited in vitro by hexachlorophene (IC50 2.05 µM) and by flavonoids/catechin gallates (noncompetitive; IC50 0.2–1.1 µM)."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"16722653","id":"PMC_16722653","title":"Inhibition of Plasmodium falciparum fatty acid biosynthesis: evaluation of FabG, FabZ, and FabI as drug targets for flavonoids.","date":"2006","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16722653","citation_count":152,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"20714430","id":"PMC_20714430","title":"Bromopyrrole alkaloids as lead compounds against protozoan parasites.","date":"2010","source":"Marine drugs","url":"https://pubmed.ncbi.nlm.nih.gov/20714430","citation_count":65,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16225460","id":"PMC_16225460","title":"Kinetic, inhibition and structural studies on 3-oxoacyl-ACP reductase from Plasmodium falciparum, a key enzyme in fatty acid biosynthesis.","date":"2006","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/16225460","citation_count":63,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3-oxoacyl-[acyl-carrier-protein] reductase","FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"12646215","id":"PMC_12646215","title":"Functional characterization of beta-ketoacyl-ACP reductase (FabG) from Plasmodium falciparum.","date":"2003","source":"Biochemical and biophysical research 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products","url":"https://pubmed.ncbi.nlm.nih.gov/23806111","citation_count":25,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18424102","id":"PMC_18424102","title":"Inhibiting enoyl-ACP reductase (FabI) across pathogenic microorganisms by linear sesquiterpene lactones from Anthemis auriculata.","date":"2008","source":"Phytomedicine : international journal of phytotherapy and phytopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/18424102","citation_count":24,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16934037","id":"PMC_16934037","title":"Analyses of co-operative transitions in Plasmodium falciparum beta-ketoacyl acyl carrier protein reductase upon co-factor and acyl carrier protein binding.","date":"2006","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/16934037","citation_count":24,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17485508","id":"PMC_17485508","title":"Mass spectrometry-based systems approach for identification of inhibitors of Plasmodium falciparum fatty acid synthase.","date":"2007","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/17485508","citation_count":21,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22951393","id":"PMC_22951393","title":"Marchantin A, a macrocyclic bisbibenzyl ether, isolated from the liverwort Marchantia polymorpha, inhibits protozoal growth in vitro.","date":"2012","source":"Phytomedicine : international journal of phytotherapy and phytopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/22951393","citation_count":17,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24591179","id":"PMC_24591179","title":"Compound prioritization from inverse docking experiment using receptor-centric and ligand-centric methods: a case study on Plasmodium falciparum Fab enzymes.","date":"2014","source":"Journal of molecular recognition : JMR","url":"https://pubmed.ncbi.nlm.nih.gov/24591179","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23727443","id":"PMC_23727443","title":"Recent developments in the antiprotozoal and anticancer activities of the 2-alkynoic fatty acids.","date":"2013","source":"Chemistry and physics of lipids","url":"https://pubmed.ncbi.nlm.nih.gov/23727443","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25103602","id":"PMC_25103602","title":"2-Octadecynoic acid as a dual life stage inhibitor of Plasmodium infections and plasmodial FAS-II enzymes.","date":"2014","source":"Bioorganic & medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/25103602","citation_count":7,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17879351","id":"PMC_17879351","title":"A unique and differential effect of denaturants on cofactor mediated activation of Plasmodium falciparum beta-ketoacyl-ACP reductase.","date":"2008","source":"Proteins","url":"https://pubmed.ncbi.nlm.nih.gov/17879351","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18721141","id":"PMC_18721141","title":"Deciphering the key residues in Plasmodium falciparum beta-ketoacyl acyl carrier protein reductase responsible for interactions with Plasmodium falciparum acyl carrier protein.","date":"2008","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/18721141","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG","PfFabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15939298","id":"PMC_15939298","title":"Production and purification of refolded recombinant Plasmodium falciparum beta-ketoacyl-ACP reductase from inclusion 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the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40791414","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41775037","id":"PMC_41775037","title":"TEpiNom: A computational framework integrating population data to prioritize Plasmodium falciparum T cell epitopes.","date":"2026","source":"Vaccine","url":"https://pubmed.ncbi.nlm.nih.gov/41775037","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["FabG"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12594,"output_tokens":2905,"usd":0.040678,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8599,"output_tokens":3987,"usd":0.071335,"stage2_stop_reason":"end_turn"},"total_usd":0.112013,"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\": 2006,\n      \"finding\": \"PfFabG (3-oxoacyl-ACP reductase) was crystallized at 1.5 Å resolution, revealing a homotetrameric structure with a catalytic triad of serine, tyrosine, and lysine aligned in an active conformation; a sulphate ion occupies the cofactor-binding site; and a cluster of positively charged residues at the active-site entrance is consistent with ACP substrate recognition. Kinetic and product inhibition studies indicated a steady-state ordered mechanism, with NADPH binding to the free enzyme first. Activity with NADH was <3% of that with NADPH. Hexachlorophene inhibited FabG with IC50 2.05 µM via non-linear competitive inhibition with respect to NADPH.\",\n      \"method\": \"X-ray crystallography (1.5 Å), fluorescence enhancement binding assays, kinetic analysis (steady-state ordered mechanism), product inhibition, in vitro enzymatic assay, inhibitor titration\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation by kinetic and inhibition assays, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"16225460\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Recombinant P. falciparum FabG expressed in E. coli is soluble and enzymatically active, catalyzing reduction of acetoacetyl-CoA with Km 75 µM, Vmax 0.0054 µmol/min/ml, and kcat 0.014 s−1. NADPH exhibits negative cooperativity in binding to FabG. Homology modeling using Brassica napus FabG as template provided a structural rationale for NADPH cofactor specificity.\",\n      \"method\": \"Recombinant protein expression in E. coli, in vitro enzymatic assay with acetoacetyl-CoA, kinetic characterization, homology modeling\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with kinetic characterization and homology modeling, single lab\",\n      \"pmids\": [\"12646215\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Binding of NADPH to PfFabG increases the binding affinity of substrate acetoacetyl-CoA by 16-fold and increases affinity for acyl carrier protein (ACP) approximately 3-fold, demonstrating ordered cofactor-mediated activation. PfFabG exhibits negative homotropic cooperativity for NADPH, which is enhanced in the presence of ACP. ACP increases NADPH accessibility to PfFabG. In the presence of NADP+, the reverse reaction is also observed (Ka = 23.17 µM−1).\",\n      \"method\": \"Intrinsic fluorescence spectroscopy (Trp334 nm), NADPH fluorescence (450 nm), acrylamide quenching assays, binding affinity measurements\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple fluorescence-based binding assays, single lab, two orthogonal readouts\",\n      \"pmids\": [\"16934037\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Arg187 and Arg230 of PfFabG are critical residues for interaction with P. falciparum ACP (PfACP). Mutagenesis of Arg187, Arg190, and Arg230 reduced affinities of PfFabG mutants for acetoacetyl-ACP (the physiological substrate) compared to wild-type, while activity with the substrate analog acetoacetyl-CoA was retained. Surface plasmon resonance and intrinsic fluorescence confirmed direct PfFabG–PfACP binding, identifying a positively charged/hydrophobic patch adjacent to the active site as the ACP interaction site.\",\n      \"method\": \"Site-directed mutagenesis, ACP-dependent and ACP-independent enzymatic assays, intrinsic fluorescence binding assays, surface plasmon resonance\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis combined with SPR and fluorescence binding assays and kinetic activity measurements, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"18721141\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The elongation module of P. falciparum FAS-II was reconstituted in vitro using all four enzymes—FabB/F, FabG, FabZ, and FabI—and the reaction products were analyzed by MALDI-TOF MS. The distribution of acyl products from the reconstituted system matched the in vivo pattern, confirming FabG participates sequentially in iterative fatty acid chain elongation. Inhibition of FabG by (-)-catechin gallate led to accumulation of the upstream intermediate, detectable by MS.\",\n      \"method\": \"In vitro reconstitution of FAS-II elongation module, MALDI-TOF MS product analysis, inhibitor perturbation assay\",\n      \"journal\": \"Antimicrobial agents and chemotherapy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with MS-based product analysis, inhibitor-intermediate accumulation confirms pathway position, single lab\",\n      \"pmids\": [\"17485508\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PfFabG is a homotetramer (Mr ~120,000) belonging to the short-chain alcohol dehydrogenase/reductase (SDR) superfamily. Guanidinium chloride-induced denaturation follows a simple A4 ↔ 4A two-state unfolding model. Conformational stability (ΔGs) is 22.68 kcal/mol with ΔCp of 5.83 kcal/(mol·K), attributed to the large tetrameric size and buried hydrophobic core.\",\n      \"method\": \"Intrinsic fluorescence spectroscopy, circular dichroism, denaturant-induced unfolding, enzymatic activity measurements, thermodynamic analysis\",\n      \"journal\": \"IUBMB life\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biophysical methods (fluorescence, CD, activity), two-state unfolding model validated by concentration independence, single lab\",\n      \"pmids\": [\"17654120\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Urea-induced unfolding of PfFabG is a multi-step process, whereas GdmCl-induced unfolding is two-state. In the presence of NADPH during urea unfolding, an activity-enhanced intermediate state is populated at ~1 M urea (90% activity recovered upon dilution), while NADPH provides no stabilization during GdmCl unfolding. NADPH binding leads to compaction of PfFabG structure as evidenced by decreased tryptophan accessibility to acrylamide quenching.\",\n      \"method\": \"Intrinsic fluorescence, circular dichroism, enzymatic activity measurement, glutaraldehyde cross-linking, size exclusion chromatography, acrylamide quenching\",\n      \"journal\": \"Proteins\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biophysical methods, single lab, cofactor-dependent conformational effect validated across assays\",\n      \"pmids\": [\"17879351\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Flavonoids inhibit PfFabG in a noncompetitive manner (luteolin and (-)-catechin gallate used as model compounds in kinetic analysis), establishing the mode of inhibition at the enzyme level. C-3 gallic acid esters of catechins are the most potent inhibitors (IC50 0.2–1.1 µM).\",\n      \"method\": \"In vitro enzyme inhibition assay, kinetic analysis (mode of inhibition determination), IC50 determination\",\n      \"journal\": \"Journal of medicinal chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — kinetic mode-of-inhibition analysis with defined compounds, single lab, inhibitor mechanism established\",\n      \"pmids\": [\"16722653\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PfFabG overexpressed in E. coli as inclusion bodies could be correctly refolded only in the presence of the cofactor NADPH and 300 mM NaCl, demonstrating that NADPH is required for proper folding of the recombinant enzyme. The refolded protein was enzymatically active with acetoacetyl-CoA.\",\n      \"method\": \"Recombinant protein expression, inclusion body refolding, enzymatic activity assay\",\n      \"journal\": \"Protein expression and purification\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single method (refolding/activity assay), cofactor-dependent folding is an indirect inference, single lab\",\n      \"pmids\": [\"15939298\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PfFabG (PF3D7_0922900) is a homotetrameric NADPH-dependent 3-oxoacyl-ACP reductase of the SDR superfamily that catalyzes the first reductive step in the P. falciparum type II fatty acid biosynthesis elongation cycle via a steady-state ordered mechanism (NADPH binds first); NADPH binding compacts the protein and increases substrate (acetoacetyl-ACP) and ACP binding affinity by 16-fold and ~3-fold respectively; Arg187 and Arg230 in a positively charged patch adjacent to the active site mediate critical interactions with the acyl carrier protein (PfACP); and the enzyme has been positioned within the FAS-II elongation module by in vitro reconstitution, where its inhibition leads to detectable accumulation of upstream intermediates.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"FabG (PF3D7_0922900) is the NADPH-dependent 3-oxoacyl-[acyl-carrier-protein] reductase that catalyzes the first reductive step of the iterative type II fatty acid biosynthesis (FAS-II) elongation cycle in Plasmodium falciparum [#0, #4]. It is a homotetramer of the short-chain dehydrogenase/reductase (SDR) superfamily with a Ser/Tyr/Lys catalytic triad and a marked preference for NADPH over NADH [#0, #5]. The enzyme operates by a steady-state ordered mechanism in which NADPH binds the free enzyme first; cofactor binding compacts the protein and increases affinity for the acetoacetyl-ACP substrate ~16-fold and for the acyl carrier protein PfACP ~3-fold, so that cofactor loading gates productive substrate engagement [#0, #2, #6]. Recognition of the physiological ACP-tethered substrate occurs through a positively charged, hydrophobic patch adjacent to the active site, with Arg187 and Arg230 mediating critical direct contacts to PfACP [#0, #3]. Within a reconstituted FAS-II elongation module (FabB/F, FabG, FabZ, FabI), FabG acts sequentially in chain elongation, and its inhibition causes accumulation of the upstream intermediate, fixing its position in the pathway [#4]. FabG is inhibited in vitro by hexachlorophene and by flavonoids, most potently C-3 gallic acid esters of catechins [#0, #7]. No genetic loss-of-function or in vivo parasite phenotype for FabG has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Establishing that the P. falciparum FabG gene product is a bona fide, soluble, catalytically active reductase was the first step in defining a candidate FAS-II enzyme; recombinant expression answered whether the annotated gene encodes a functional 3-oxoacyl reductase.\",\n      \"evidence\": \"recombinant expression in E. coli with in vitro kinetics on acetoacetyl-CoA and homology modeling\",\n      \"pmids\": [\"12646215\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"kinetics measured on the CoA analog rather than the physiological ACP-linked substrate\",\n        \"no structural data to confirm the modeled NADPH specificity\",\n        \"cellular role in the parasite not addressed\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Refolding experiments probed the relationship between cofactor and enzyme integrity, showing NADPH is not merely catalytic but is required for correct folding of the recombinant enzyme.\",\n      \"evidence\": \"inclusion-body refolding restored only in the presence of NADPH and NaCl, with activity readout\",\n      \"pmids\": [\"15939298\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"cofactor-dependent folding is an indirect inference from a single refolding/activity assay\",\n        \"does not establish whether native in vivo folding requires NADPH\",\n        \"no structural characterization of the refolded species\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"The 1.5 Å crystal structure resolved the catalytic architecture and cofactor logic, answering how the enzyme is organized and why it prefers NADPH — defining the Ser/Tyr/Lys triad, the tetrameric assembly, and a steady-state ordered mechanism with NADPH binding first.\",\n      \"evidence\": \"X-ray crystallography with kinetic and product-inhibition analysis and inhibitor titration (hexachlorophene)\",\n      \"pmids\": [\"16225460\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"cofactor site occupied by sulphate rather than NADPH, so cofactor-bound conformation inferred\",\n        \"no co-crystal with ACP or acyl substrate\",\n        \"ACP recognition inferred from surface charge, not directly visualized\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Binding studies established the allosteric consequence of the ordered mechanism — that NADPH loading actively primes the enzyme for substrate and ACP engagement — explaining how cofactor order translates into catalytic control.\",\n      \"evidence\": \"intrinsic and NADPH fluorescence, acrylamide quenching, and affinity measurements\",\n      \"pmids\": [\"16934037\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"negative cooperativity for NADPH not linked to a structural transition\",\n        \"physiological relevance of the observed reverse reaction unclear\",\n        \"single-lab fluorescence approach\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Kinetic mode-of-inhibition analysis of flavonoids defined FabG as a druggable target and characterized how flavonoid inhibitors act, identifying noncompetitive inhibition and the most potent chemical class.\",\n      \"evidence\": \"in vitro enzyme inhibition kinetics and IC50 determination for catechin/flavonoid series\",\n      \"pmids\": [\"16722653\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"inhibition characterized only in vitro, not in parasites\",\n        \"binding site of noncompetitive inhibitors not mapped\",\n        \"selectivity over host reductases not established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"In vitro reconstitution of the full FAS-II elongation module placed FabG in the sequential elongation cycle, answering where in the pathway the enzyme acts by showing its inhibition stalls the cycle at an upstream intermediate.\",\n      \"evidence\": \"reconstitution of FabB/F, FabG, FabZ, FabI with MALDI-TOF product profiling and inhibitor perturbation\",\n      \"pmids\": [\"17485508\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"pathway assembled in vitro rather than in the parasite\",\n        \"does not address regulation of the cycle in vivo\",\n        \"no genetic confirmation of FabG requirement\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Biophysical characterization defined the enzyme's oligomeric state and stability, confirming a homotetrameric SDR-family protein with a two-state GdmCl unfolding transition.\",\n      \"evidence\": \"fluorescence, CD, denaturant unfolding, and thermodynamic analysis\",\n      \"pmids\": [\"17654120\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"stability measured on recombinant protein only\",\n        \"does not connect fold stability to catalytic regulation\",\n        \"single-lab thermodynamic model\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Unfolding studies with cofactor revealed that NADPH binding compacts the enzyme and populates an activity-enhanced intermediate, linking cofactor binding to a defined conformational change.\",\n      \"evidence\": \"urea vs GdmCl unfolding with CD, fluorescence, cross-linking, SEC and acrylamide quenching\",\n      \"pmids\": [\"17879351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"compaction inferred from indirect quenching/unfolding readouts\",\n        \"structural basis of the intermediate not resolved\",\n        \"physiological significance of the intermediate state unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Mutagenesis identified the specific residues mediating recognition of the physiological ACP-tethered substrate, answering how FabG discriminates ACP-linked acetoacetyl from the free CoA analog — Arg187 and Arg230 form the PfACP interaction site.\",\n      \"evidence\": \"site-directed mutagenesis with ACP-dependent vs ACP-independent activity, SPR, and fluorescence binding\",\n      \"pmids\": [\"18721141\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"ACP-bound complex not structurally resolved\",\n        \"mutant catalytic mechanism retained on CoA analog, so effect is on ACP docking only\",\n        \"no in vivo test of these residues\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The in vivo essentiality, genetic loss-of-function phenotype, and validation of FabG as an antimalarial drug target in the intact parasite remain unaddressed in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"no gene knockout or conditional knockdown reported\",\n        \"no demonstration that inhibitors kill parasites via FabG\",\n        \"no structure of the FabG–PfACP or FabG–NADPH complex\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004316\", \"supporting_discovery_ids\": [0, 1, 3, 4]},\n      {\"term_id\": \"GO:0050661\", \"supporting_discovery_ids\": [0, 2, 6]},\n      {\"term_id\": \"GO:0016616\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006633\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0009245\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\n      \"Homotetramer (FabG A4 assembly)\",\n      \"FAS-II elongation module (with FabB/F, FabZ, FabI; in vitro reconstitution)\"\n    ],\n    \"partners\": [\n      \"PfACP (acyl carrier protein; direct binding via Arg187/Arg230)\",\n      \"NADPH (cofactor)\"\n    ],\n    \"other_free_text\": [\n      \"SDR superfamily member with Ser/Tyr/Lys catalytic triad.\",\n      \"Steady-state ordered mechanism: NADPH binds free enzyme first; NADPH increases acetoacetyl-ACP affinity ~16-fold and ACP affinity ~3-fold.\",\n      \"Exhibits negative homotropic cooperativity for NADPH, enhanced by ACP.\",\n      \"NADPH binding compacts the protein and stabilizes an activity-enhanced intermediate.\",\n      \"Inhibited in vitro by hexachlorophene (IC50 2.05 µM) and by flavonoids/catechin gallates (noncompetitive; IC50 0.2–1.1 µM).\"\n    ]\n  }\n}\n```","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0922900","name":null,"product":"3-oxoacyl-[acyl-carrier-protein] reductase","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0823800","name":null,"product":"3-oxoacyl-[acyl-carrier-protein] reductase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0720900","name":null,"product":"3-oxoacyl-[acyl-carrier-protein] reductase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"FabG","evaluation":null}