{"gene":"PF3D7_0621200","run_date":"2026-09-08T12:51:26","timeline":{"discoveries":[{"year":2004,"finding":"PDX1 (PfPdx1) and PfPdx2 together catalyze de novo vitamin B6 biosynthesis in P. falciparum; the two proteins act together in glutaminase activity with a specific activity of 209 nmol min⁻¹ mg⁻¹ and a Km for glutamine of 1.3 mM. Complementation of pyridoxine-auxotrophic yeast confirmed functional activity of PfPdx1 in vivo.","method":"Recombinant protein biochemistry (glutaminase assay), yeast complementation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay with kinetic parameters plus in vivo yeast complementation, single lab but two orthogonal methods","pmids":["15590634"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"PDX1 (PfPdx1) is the pyridoxal-5'-phosphate synthase catalytic domain; it requires complex formation with PfPdx2 (glutaminase subunit) for catalytic activity of either domain. PDX1 can form a chimeric bi-enzyme with bacterial YaaE (a Pdx2 ortholog) both in vivo and in vitro, but this chimera does not attain full catalytic activity, indicating species-specific structural features govern partner interaction.","method":"Recombinant protein biochemistry, in vitro reconstitution, chimeric protein assay, crystal structure of Pdx2 at 1.62 Å","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution combined with structural determination and chimera functional analysis, single lab with multiple orthogonal methods","pmids":["16339145"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"Complex formation between PDX1 (PfPdx1) and PfPdx2 is governed by hydrophobic interactions at the interface; l-glutamine binding increases the tightness of the PfPdx1–PfPdx2 interaction ~30-fold. The N-terminal αN-helix of PfPdx1 is required for complex formation; a 'swap mutant' in which the αN-helix was replaced with the B. subtilis segment gained cross-binding to BsPdx2 and partially elicited BsPdx2 glutaminase activity, linking complex interface formation to catalytic activation of the glutaminase.","method":"Isothermal titration calorimetry (ITC), 3D homology modelling, swap mutagenesis with glutaminase activity assay","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — ITC thermodynamics, mutagenesis, and functional assay in a single study; single lab but multiple orthogonal methods","pmids":["17950752"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"Residues R85, H88, and E91 at the PDX1:PDX1 interface are required for dodecameric complex assembly; alanine substitutions at these positions impede both PDX1 activity and PfPdx2 binding, yielding a monomeric protein. Catalytic-site residues D26, K83, and K151 are required for enzymatic activity; mutation to alanine results in a hexameric (not dodecameric) assembly and does not affect Pdx2 binding or its activity. K151 is specifically required for the transition from hexamer to functional dodecamer.","method":"Site-directed mutagenesis, gel filtration (oligomeric state analysis), enzyme activity assay, co-purification with PfPdx2","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — mutagenesis with biochemical characterization of oligomeric states and activity, multiple residues tested with orthogonal readouts, single lab","pmids":["18350152"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"finding":"Glycine 155 of PDX1 is required for the transition from hexameric to dodecameric assembly; a G155A substitution results in a hexameric protein with altered secondary structure (by CD) that retains the ability to bind PfPdx2 and support its glutaminase activity, but cannot form the active dodecamer, demonstrating that structural flexibility at this position is necessary for dodecamer formation and full enzymatic activity.","method":"Static and dynamic light scattering, circular dichroism, co-purification, enzyme assay","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 1 / Moderate — mutagenesis with multiple orthogonal biophysical and biochemical methods, single lab","pmids":["19272411"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2010,"finding":"The C-terminus of PDX1 has four distinct and separable functions: assembly of PDX1 monomers, binding of the pentose substrate ribose 5-phosphate (R5P), formation of the reaction intermediate I₃₂₀, and final PLP synthesis. PLP formation is the only function conferred to the enzyme by the C-terminus acting in trans, explaining the cooperative nature of the complex.","method":"C-terminal deletion analysis, biochemical assays for intermediate formation and PLP production, intersubunit complementation","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic deletion analysis with multiple functional readouts distinguishing individual biochemical steps, single lab","pmids":["20837012"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"PDX1 and PfPdx2 interact in vivo in P. falciparum intraerythrocytic parasites, demonstrated by pull-down of transgenic parasites overexpressing both proteins. Overexpression of the PDX1/PfPdx2 complex raises intracellular PLP levels from 12.5 µM (wild-type) to 36.6 µM and confers increased tolerance to singlet oxygen (¹O₂). Dominant-negative inactive mutants of PDX1 and PfPdx2 rendered parasites susceptible to ¹O₂, establishing a role for PDX1-mediated PLP biosynthesis in antioxidant defence.","method":"In vivo pull-down from transgenic parasites, live-cell fluorescence microscopy, PLP quantification, dominant-negative mutagenesis","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — in vivo pull-down with transgenic parasites, quantitative PLP measurement, dominant-negative phenotype, multiple orthogonal methods in single lab","pmids":["22242896"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"The cryo-EM structure of the P. falciparum PLP synthase complex reveals random association of up to 12 PfPdx2 glutaminase subunits to the dodecameric PDX1 core. Plasmodium PLP synthase uniquely organizes into fibers. Crystal structure shows alternative positioning of an α-helix distinguishing open vs. closed conformations upon substrate binding; the pentose substrate is covalently attached at C1, forming a Schiff base with Lys84 of PDX1. A transient ammonia-transfer tunnel between PfPdx2 glutaminase and PDX1 active sites is regulated during catalysis. Mutagenesis defined critical methionines required for complex formation.","method":"Cryo-EM, X-ray crystallography, site-directed mutagenesis","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure and EM structure with mutagenesis validation, multiple orthogonal structural methods, single lab","pmids":["22244765"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"D-erythrose 4-phosphate (E4P) inhibits PDX1 enzymatic activity in a dose-dependent manner, likely by interfering with ribose 5-phosphate (R5P) imine bond formations at the active site. The E4P hydrazide analogue 4PEHz selectively inhibits PDX1 with IC50 43 µM (free enzyme) and 16 µM in the heteromeric PLP synthase complex. Transgenic P. falciparum overexpressing PDX1 and PfPdx2 showed protection against 4PEHz, confirming on-target activity in vivo.","method":"In vitro enzyme inhibition assay, molecular docking, transgenic parasite overexpression protection assay, P. falciparum culture IC50","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay with mechanistic rationale, in vivo target validation via overexpression rescue, multiple methods, single lab","pmids":["23039077"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"finding":"In P. vivax, the PDX1 ortholog (Pdx1) forms a dodecameric complex and, when mixed with Pdx2, assembles into a ring-shaped, monodispersed 24-meric (dodecameric Pdx1 core decorated with Pdx2) heteromeric complex, as determined by DLS, SAXS, and EM. Pdx2 alone exists in monomeric and various oligomeric states but forms a monodispersed complex upon mixing with dodecameric Pdx1.","method":"Dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), electron microscopy (EM)","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biophysical methods on purified complex, single lab; structural characterization without mutagenesis validation","pmids":["32825141"],"is_preprint":false,"attribution":[{"species":"Plasmodium vivax","strain":""}]},{"year":2022,"finding":"DATP 18 (3,5-bis(quinolin-4-ylmethylene)tetrahydro-2H-pyran-4(3H)-one) inhibits PDX1 enzymatic activity with IC50 20.34 µM in vitro, approximately twofold more potent than the previously known inhibitor 4PEHz (IC50 43 µM), establishing PDX1 as the molecular target of this compound class.","method":"In vitro enzyme inhibition assay","journal":"ChemMedChem","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single in vitro enzyme assay, no in vivo target validation for PDX1 specifically, single study","pmids":["36251345"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PDX1 (PF3D7_0621200) is the pyridoxal 5'-phosphate (PLP) synthase catalytic subunit in P. falciparum that oligomerizes into a dodecameric core and recruits up to 12 PfPdx2 glutaminase subunits to form a heteromeric 24-mer; ammonia generated by PfPdx2 is channelled through a transient tunnel to the PDX1 active site, where ribose 5-phosphate and glyceraldehyde 3-phosphate are condensed via sequential Schiff-base intermediates (anchored at Lys84) to produce PLP, with complex assembly—governed by interface residues R85/H88/E91, the αN-helix, and the C-terminus—being obligatory for catalytic activity; the resulting de novo PLP serves both as an essential enzyme cofactor and as an antioxidant to detoxify singlet oxygen generated during haemoglobin digestion."},"narrative":{"mechanistic_narrative":"PDX1 (PF3D7_0621200) is the pyridoxal 5'-phosphate (PLP) synthase catalytic subunit of the de novo vitamin B6 biosynthetic pathway in Plasmodium falciparum, acting together with the glutaminase subunit PfPdx2 [PMID:15590634]. PDX1 provides the synthase domain that condenses ribose 5-phosphate and a triose substrate into PLP, anchoring the pentose via a Schiff base at Lys84, while ammonia generated by PfPdx2 is channelled to the PDX1 active site through a transient interdomain tunnel; either domain requires complex formation for activity [PMID:16339145, PMID:22244765]. Assembly proceeds hierarchically: PDX1 monomers build a dodecameric core that recruits up to twelve PfPdx2 glutaminase subunits to form the heteromeric synthase, with the PDX1:PDX1 interface residues R85/H88/E91, the N-terminal αN-helix, glycine residues G155 governing the hexamer-to-dodecamer transition, and the C-terminus all being obligatory for oligomerization and catalysis [PMID:17950752, PMID:18350152, PMID:19272411, PMID:20837012]. In intraerythrocytic parasites PDX1 and PfPdx2 interact in vivo, and PDX1-driven PLP production not only supplies an essential enzyme cofactor but also confers tolerance to singlet oxygen, defining an antioxidant role during the blood stage [PMID:22242896]. Because this pathway is absent in the human host, PDX1 is a validated antimalarial target: the substrate-analogue inhibitor 4PEHz acts on-target in vivo [PMID:23039077], and additional inhibitor scaffolds have been shown to block its activity [PMID:36251345].","teleology":[{"year":2004,"claim":"Establishing whether malaria parasites synthesize vitamin B6 de novo, the first work showed PDX1 and PfPdx2 jointly catalyze this pathway, defining PDX1 as a functional biosynthetic enzyme.","evidence":"Recombinant glutaminase assay with kinetic parameters plus complementation of pyridoxine-auxotrophic yeast","pmids":["15590634"],"confidence":"High","gaps":["Did not resolve the individual catalytic step performed by PDX1 versus PfPdx2","No structural basis for the interaction"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"claim":"To determine whether PDX1 is catalytically autonomous, reconstitution showed PDX1 is the PLP synthase catalytic domain but requires complex formation with PfPdx2 for either domain to function, and that partner recognition carries species-specific structural features.","evidence":"In vitro reconstitution, chimeric enzyme with bacterial YaaE, and crystal structure of Pdx2","pmids":["16339145"],"confidence":"High","gaps":["Molecular determinants of species-specific partner selection not yet mapped","No structure of PDX1 itself"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"To dissect how the two subunits associate and communicate, ITC and swap mutagenesis showed the interaction is hydrophobic and glutamine-tightened, with the PDX1 αN-helix required for complex formation and coupled to glutaminase activation.","evidence":"Isothermal titration calorimetry, homology modelling, and αN-helix swap mutagenesis with glutaminase assay","pmids":["17950752"],"confidence":"High","gaps":["Thermodynamics based on modelling rather than an experimental PDX1 structure","Allosteric path from interface to glutaminase site not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"To map residues governing assembly versus catalysis, mutagenesis separated interface residues (R85/H88/E91) required for dodecamer formation and PfPdx2 binding from active-site residues (D26/K83/K151) required for activity, with K151 driving the hexamer-to-dodecamer transition.","evidence":"Site-directed mutagenesis with gel filtration, activity assays, and co-purification with PfPdx2","pmids":["18350152"],"confidence":"High","gaps":["Structural mechanism linking dodecamerization to activity not visualized","Whether hexamer is a physiological intermediate unclear"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"claim":"Extending the assembly model, G155 was shown to enable the hexamer-to-dodecamer transition, since G155A retains PfPdx2 binding and glutaminase support but cannot form the active dodecamer.","evidence":"Light scattering, circular dichroism, co-purification and enzyme assays on the G155A mutant","pmids":["19272411"],"confidence":"High","gaps":["Conformational change enabled by G155 flexibility not directly observed","Kinetics of the oligomeric transition unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2010,"claim":"To assign the biochemical roles of the PDX1 C-terminus, deletion analysis resolved four separable functions—monomer assembly, R5P binding, I320 intermediate formation, and PLP synthesis—with PLP synthesis provided in trans, explaining complex cooperativity.","evidence":"C-terminal deletion analysis with intermediate/PLP assays and intersubunit complementation","pmids":["20837012"],"confidence":"High","gaps":["Structural view of the C-terminal trans-acting contribution absent","Order of substrate binding relative to assembly not fully defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"To establish physiological relevance, in vivo work showed PDX1 and PfPdx2 interact in parasites, that complex overexpression raises PLP and singlet-oxygen tolerance, and that dominant-negative mutants sensitize parasites, linking PDX1 to antioxidant defence.","evidence":"In vivo pull-down from transgenic parasites, PLP quantification, and dominant-negative phenotyping","pmids":["22242896"],"confidence":"High","gaps":["Whether antioxidant role reflects PLP directly or downstream PLP-dependent enzymes not separated","Genetic essentiality of PDX1 not tested by knockout"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"To visualize the assembled machine, structural work resolved a dodecameric PDX1 core randomly decorated with up to 12 PfPdx2 subunits, the pentose Schiff base at Lys84, open/closed conformations, and a regulated transient ammonia tunnel, plus fiber organization unique to Plasmodium.","evidence":"Cryo-EM, X-ray crystallography, and site-directed mutagenesis of interface methionines","pmids":["22244765"],"confidence":"High","gaps":["Functional significance of the fiber arrangement in vivo unknown","Dynamics of tunnel gating during turnover not directly captured"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"To pursue PDX1 as a drug target, E4P and its hydrazide 4PEHz were shown to inhibit the enzyme and complex, with overexpression protecting parasites, providing in vivo on-target validation.","evidence":"In vitro inhibition assays, docking, transgenic overexpression protection, and parasite culture IC50","pmids":["23039077"],"confidence":"High","gaps":["Whole-cell potency and selectivity of 4PEHz modest","No co-structure of inhibitor bound to PDX1"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"claim":"To test conservation of the assembly across species, the P. vivax PDX1 ortholog was shown to form a dodecameric core that assembles with Pdx2 into a monodisperse ring-shaped 24-mer.","evidence":"DLS, SAXS, and EM on purified P. vivax Pdx1/Pdx2","pmids":["32825141"],"confidence":"Medium","gaps":["No mutagenesis or activity validation of the P. vivax complex","Catalytic parameters for P. vivax PDX1 not measured"],"attribution":[{"species":"Plasmodium vivax","strain":""}]},{"year":2022,"claim":"To broaden the inhibitor chemical space, DATP 18 was shown to inhibit PDX1 with ~twofold greater in vitro potency than 4PEHz, nominating a new scaffold against the enzyme.","evidence":"Single in vitro enzyme inhibition assay","pmids":["36251345"],"confidence":"Low","gaps":["No in vivo target validation for PDX1 with this compound","Selectivity and whole-parasite activity not established","Binding mode not determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PDX1 is genetically essential for blood-stage growth by direct gene knockout, and the structural basis of inhibitor binding, remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No conditional knockout or genetic essentiality data in the corpus","No inhibitor-bound co-structure of PDX1"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Heteromeric PLP synthase complex (dodecameric PDX1 core + up to 12 PfPdx2 glutaminase subunits, 24-mer)"],"partners":["PFPDX2 (GLUTAMINASE SUBUNIT)"],"other_free_text":["Pentose substrate ribose 5-phosphate forms a Schiff base at Lys84 of PDX1 [#7]","Interface residues R85/H88/E91 required for dodecamer assembly and PfPdx2 binding; D26/K83/K151 required for catalysis [#3]","G155 flexibility required for hexamer-to-dodecamer transition [#4]; N-terminal αN-helix required for complex formation [#2]; C-terminus provides monomer assembly, R5P binding, I320 intermediate formation and trans PLP synthesis [#5]","Inhibited by E4P/4PEHz (substrate analogue, on-target in vivo) [#8] and DATP 18 scaffold [#10]","P. vivax PDX1 ortholog forms an analogous dodecameric core / 24-mer with Pdx2 [#9]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"15590634","id":"PMC_15590634","title":"Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasite Plasmodium falciparum.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15590634","citation_count":69,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1","PfPDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"16339145","id":"PMC_16339145","title":"Vitamin B6 biosynthesis by the malaria parasite Plasmodium falciparum: biochemical and structural insights.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16339145","citation_count":65,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22244765","id":"PMC_22244765","title":"Assembly of the eukaryotic PLP-synthase complex from Plasmodium and activation of the Pdx1 enzyme.","date":"2012","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/22244765","citation_count":26,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22242896","id":"PMC_22242896","title":"The antioxidative effect of de novo generated vitamin B6 in Plasmodium falciparum validated by protein interference.","date":"2012","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/22242896","citation_count":25,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18350152","id":"PMC_18350152","title":"The assembly of the plasmodial PLP synthase complex follows a defined course.","date":"2008","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/18350152","citation_count":18,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23039077","id":"PMC_23039077","title":"Exploring inhibition of Pdx1, a component of the PLP synthase complex of the human malaria parasite Plasmodium falciparum.","date":"2013","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/23039077","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1","PfPDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17950752","id":"PMC_17950752","title":"Structural and thermodynamic insights into the assembly of the heteromeric pyridoxal phosphate synthase from Plasmodium falciparum.","date":"2007","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17950752","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1","PfPDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19272411","id":"PMC_19272411","title":"Mobility of the conserved glycine 155 is required for formation of the active plasmodial Pdx1 dodecamer.","date":"2009","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/19272411","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"20837012","id":"PMC_20837012","title":"Defining the structural requirements for ribose 5-phosphate-binding and intersubunit cross-talk of the malarial pyridoxal 5-phosphate synthase.","date":"2010","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/20837012","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32825141","id":"PMC_32825141","title":"Solution Structures and Dynamic Assembly of the 24-Meric Plasmodial Pdx1-Pdx2 Complex.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32825141","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34327152","id":"PMC_34327152","title":"Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions.","date":"2021","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34327152","citation_count":3,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36251345","id":"PMC_36251345","title":"Antiplasmodial and Antimalarial Activity of 3,5-Diarylidenetetrahydro-2H-pyran-4(3H)-ones via Inhibition of Plasmodium falciparum Pyridoxal Synthase.","date":"2022","source":"ChemMedChem","url":"https://pubmed.ncbi.nlm.nih.gov/36251345","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfPDX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9165,"output_tokens":3527,"usd":0.0402,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9417,"output_tokens":4355,"usd":0.07798,"stage2_stop_reason":"end_turn"},"total_usd":0.11818,"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\": 2004,\n      \"finding\": \"PDX1 (PfPdx1) and PfPdx2 together catalyze de novo vitamin B6 biosynthesis in P. falciparum; the two proteins act together in glutaminase activity with a specific activity of 209 nmol min⁻¹ mg⁻¹ and a Km for glutamine of 1.3 mM. Complementation of pyridoxine-auxotrophic yeast confirmed functional activity of PfPdx1 in vivo.\",\n      \"method\": \"Recombinant protein biochemistry (glutaminase assay), yeast complementation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay with kinetic parameters plus in vivo yeast complementation, single lab but two orthogonal methods\",\n      \"pmids\": [\"15590634\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PDX1 (PfPdx1) is the pyridoxal-5'-phosphate synthase catalytic domain; it requires complex formation with PfPdx2 (glutaminase subunit) for catalytic activity of either domain. PDX1 can form a chimeric bi-enzyme with bacterial YaaE (a Pdx2 ortholog) both in vivo and in vitro, but this chimera does not attain full catalytic activity, indicating species-specific structural features govern partner interaction.\",\n      \"method\": \"Recombinant protein biochemistry, in vitro reconstitution, chimeric protein assay, crystal structure of Pdx2 at 1.62 Å\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution combined with structural determination and chimera functional analysis, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"16339145\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Complex formation between PDX1 (PfPdx1) and PfPdx2 is governed by hydrophobic interactions at the interface; l-glutamine binding increases the tightness of the PfPdx1–PfPdx2 interaction ~30-fold. The N-terminal αN-helix of PfPdx1 is required for complex formation; a 'swap mutant' in which the αN-helix was replaced with the B. subtilis segment gained cross-binding to BsPdx2 and partially elicited BsPdx2 glutaminase activity, linking complex interface formation to catalytic activation of the glutaminase.\",\n      \"method\": \"Isothermal titration calorimetry (ITC), 3D homology modelling, swap mutagenesis with glutaminase activity assay\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — ITC thermodynamics, mutagenesis, and functional assay in a single study; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17950752\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Residues R85, H88, and E91 at the PDX1:PDX1 interface are required for dodecameric complex assembly; alanine substitutions at these positions impede both PDX1 activity and PfPdx2 binding, yielding a monomeric protein. Catalytic-site residues D26, K83, and K151 are required for enzymatic activity; mutation to alanine results in a hexameric (not dodecameric) assembly and does not affect Pdx2 binding or its activity. K151 is specifically required for the transition from hexamer to functional dodecamer.\",\n      \"method\": \"Site-directed mutagenesis, gel filtration (oligomeric state analysis), enzyme activity assay, co-purification with PfPdx2\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis with biochemical characterization of oligomeric states and activity, multiple residues tested with orthogonal readouts, single lab\",\n      \"pmids\": [\"18350152\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Glycine 155 of PDX1 is required for the transition from hexameric to dodecameric assembly; a G155A substitution results in a hexameric protein with altered secondary structure (by CD) that retains the ability to bind PfPdx2 and support its glutaminase activity, but cannot form the active dodecamer, demonstrating that structural flexibility at this position is necessary for dodecamer formation and full enzymatic activity.\",\n      \"method\": \"Static and dynamic light scattering, circular dichroism, co-purification, enzyme assay\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis with multiple orthogonal biophysical and biochemical methods, single lab\",\n      \"pmids\": [\"19272411\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The C-terminus of PDX1 has four distinct and separable functions: assembly of PDX1 monomers, binding of the pentose substrate ribose 5-phosphate (R5P), formation of the reaction intermediate I₃₂₀, and final PLP synthesis. PLP formation is the only function conferred to the enzyme by the C-terminus acting in trans, explaining the cooperative nature of the complex.\",\n      \"method\": \"C-terminal deletion analysis, biochemical assays for intermediate formation and PLP production, intersubunit complementation\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic deletion analysis with multiple functional readouts distinguishing individual biochemical steps, single lab\",\n      \"pmids\": [\"20837012\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PDX1 and PfPdx2 interact in vivo in P. falciparum intraerythrocytic parasites, demonstrated by pull-down of transgenic parasites overexpressing both proteins. Overexpression of the PDX1/PfPdx2 complex raises intracellular PLP levels from 12.5 µM (wild-type) to 36.6 µM and confers increased tolerance to singlet oxygen (¹O₂). Dominant-negative inactive mutants of PDX1 and PfPdx2 rendered parasites susceptible to ¹O₂, establishing a role for PDX1-mediated PLP biosynthesis in antioxidant defence.\",\n      \"method\": \"In vivo pull-down from transgenic parasites, live-cell fluorescence microscopy, PLP quantification, dominant-negative mutagenesis\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo pull-down with transgenic parasites, quantitative PLP measurement, dominant-negative phenotype, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"22242896\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The cryo-EM structure of the P. falciparum PLP synthase complex reveals random association of up to 12 PfPdx2 glutaminase subunits to the dodecameric PDX1 core. Plasmodium PLP synthase uniquely organizes into fibers. Crystal structure shows alternative positioning of an α-helix distinguishing open vs. closed conformations upon substrate binding; the pentose substrate is covalently attached at C1, forming a Schiff base with Lys84 of PDX1. A transient ammonia-transfer tunnel between PfPdx2 glutaminase and PDX1 active sites is regulated during catalysis. Mutagenesis defined critical methionines required for complex formation.\",\n      \"method\": \"Cryo-EM, X-ray crystallography, site-directed mutagenesis\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure and EM structure with mutagenesis validation, multiple orthogonal structural methods, single lab\",\n      \"pmids\": [\"22244765\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"D-erythrose 4-phosphate (E4P) inhibits PDX1 enzymatic activity in a dose-dependent manner, likely by interfering with ribose 5-phosphate (R5P) imine bond formations at the active site. The E4P hydrazide analogue 4PEHz selectively inhibits PDX1 with IC50 43 µM (free enzyme) and 16 µM in the heteromeric PLP synthase complex. Transgenic P. falciparum overexpressing PDX1 and PfPdx2 showed protection against 4PEHz, confirming on-target activity in vivo.\",\n      \"method\": \"In vitro enzyme inhibition assay, molecular docking, transgenic parasite overexpression protection assay, P. falciparum culture IC50\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay with mechanistic rationale, in vivo target validation via overexpression rescue, multiple methods, single lab\",\n      \"pmids\": [\"23039077\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In P. vivax, the PDX1 ortholog (Pdx1) forms a dodecameric complex and, when mixed with Pdx2, assembles into a ring-shaped, monodispersed 24-meric (dodecameric Pdx1 core decorated with Pdx2) heteromeric complex, as determined by DLS, SAXS, and EM. Pdx2 alone exists in monomeric and various oligomeric states but forms a monodispersed complex upon mixing with dodecameric Pdx1.\",\n      \"method\": \"Dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), electron microscopy (EM)\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biophysical methods on purified complex, single lab; structural characterization without mutagenesis validation\",\n      \"pmids\": [\"32825141\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium vivax\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DATP 18 (3,5-bis(quinolin-4-ylmethylene)tetrahydro-2H-pyran-4(3H)-one) inhibits PDX1 enzymatic activity with IC50 20.34 µM in vitro, approximately twofold more potent than the previously known inhibitor 4PEHz (IC50 43 µM), establishing PDX1 as the molecular target of this compound class.\",\n      \"method\": \"In vitro enzyme inhibition assay\",\n      \"journal\": \"ChemMedChem\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single in vitro enzyme assay, no in vivo target validation for PDX1 specifically, single study\",\n      \"pmids\": [\"36251345\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PDX1 (PF3D7_0621200) is the pyridoxal 5'-phosphate (PLP) synthase catalytic subunit in P. falciparum that oligomerizes into a dodecameric core and recruits up to 12 PfPdx2 glutaminase subunits to form a heteromeric 24-mer; ammonia generated by PfPdx2 is channelled through a transient tunnel to the PDX1 active site, where ribose 5-phosphate and glyceraldehyde 3-phosphate are condensed via sequential Schiff-base intermediates (anchored at Lys84) to produce PLP, with complex assembly—governed by interface residues R85/H88/E91, the αN-helix, and the C-terminus—being obligatory for catalytic activity; the resulting de novo PLP serves both as an essential enzyme cofactor and as an antioxidant to detoxify singlet oxygen generated during haemoglobin digestion.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PDX1 (PF3D7_0621200) is the pyridoxal 5'-phosphate (PLP) synthase catalytic subunit of the de novo vitamin B6 biosynthetic pathway in Plasmodium falciparum, acting together with the glutaminase subunit PfPdx2 [#0]. PDX1 provides the synthase domain that condenses ribose 5-phosphate and a triose substrate into PLP, anchoring the pentose via a Schiff base at Lys84, while ammonia generated by PfPdx2 is channelled to the PDX1 active site through a transient interdomain tunnel; either domain requires complex formation for activity [#1, #7]. Assembly proceeds hierarchically: PDX1 monomers build a dodecameric core that recruits up to twelve PfPdx2 glutaminase subunits to form the heteromeric synthase, with the PDX1:PDX1 interface residues R85/H88/E91, the N-terminal \\u03b1N-helix, glycine residues G155 governing the hexamer-to-dodecamer transition, and the C-terminus all being obligatory for oligomerization and catalysis [#2, #3, #4, #5]. In intraerythrocytic parasites PDX1 and PfPdx2 interact in vivo, and PDX1-driven PLP production not only supplies an essential enzyme cofactor but also confers tolerance to singlet oxygen, defining an antioxidant role during the blood stage [#6]. Because this pathway is absent in the human host, PDX1 is a validated antimalarial target: the substrate-analogue inhibitor 4PEHz acts on-target in vivo [#8], and additional inhibitor scaffolds have been shown to block its activity [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing whether malaria parasites synthesize vitamin B6 de novo, the first work showed PDX1 and PfPdx2 jointly catalyze this pathway, defining PDX1 as a functional biosynthetic enzyme.\",\n      \"evidence\": \"Recombinant glutaminase assay with kinetic parameters plus complementation of pyridoxine-auxotrophic yeast\",\n      \"pmids\": [\"15590634\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the individual catalytic step performed by PDX1 versus PfPdx2\", \"No structural basis for the interaction\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"To determine whether PDX1 is catalytically autonomous, reconstitution showed PDX1 is the PLP synthase catalytic domain but requires complex formation with PfPdx2 for either domain to function, and that partner recognition carries species-specific structural features.\",\n      \"evidence\": \"In vitro reconstitution, chimeric enzyme with bacterial YaaE, and crystal structure of Pdx2\",\n      \"pmids\": [\"16339145\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular determinants of species-specific partner selection not yet mapped\", \"No structure of PDX1 itself\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"To dissect how the two subunits associate and communicate, ITC and swap mutagenesis showed the interaction is hydrophobic and glutamine-tightened, with the PDX1 \\u03b1N-helix required for complex formation and coupled to glutaminase activation.\",\n      \"evidence\": \"Isothermal titration calorimetry, homology modelling, and \\u03b1N-helix swap mutagenesis with glutaminase assay\",\n      \"pmids\": [\"17950752\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Thermodynamics based on modelling rather than an experimental PDX1 structure\", \"Allosteric path from interface to glutaminase site not defined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"To map residues governing assembly versus catalysis, mutagenesis separated interface residues (R85/H88/E91) required for dodecamer formation and PfPdx2 binding from active-site residues (D26/K83/K151) required for activity, with K151 driving the hexamer-to-dodecamer transition.\",\n      \"evidence\": \"Site-directed mutagenesis with gel filtration, activity assays, and co-purification with PfPdx2\",\n      \"pmids\": [\"18350152\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural mechanism linking dodecamerization to activity not visualized\", \"Whether hexamer is a physiological intermediate unclear\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Extending the assembly model, G155 was shown to enable the hexamer-to-dodecamer transition, since G155A retains PfPdx2 binding and glutaminase support but cannot form the active dodecamer.\",\n      \"evidence\": \"Light scattering, circular dichroism, co-purification and enzyme assays on the G155A mutant\",\n      \"pmids\": [\"19272411\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conformational change enabled by G155 flexibility not directly observed\", \"Kinetics of the oligomeric transition unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"To assign the biochemical roles of the PDX1 C-terminus, deletion analysis resolved four separable functions\\u2014monomer assembly, R5P binding, I320 intermediate formation, and PLP synthesis\\u2014with PLP synthesis provided in trans, explaining complex cooperativity.\",\n      \"evidence\": \"C-terminal deletion analysis with intermediate/PLP assays and intersubunit complementation\",\n      \"pmids\": [\"20837012\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural view of the C-terminal trans-acting contribution absent\", \"Order of substrate binding relative to assembly not fully defined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"To establish physiological relevance, in vivo work showed PDX1 and PfPdx2 interact in parasites, that complex overexpression raises PLP and singlet-oxygen tolerance, and that dominant-negative mutants sensitize parasites, linking PDX1 to antioxidant defence.\",\n      \"evidence\": \"In vivo pull-down from transgenic parasites, PLP quantification, and dominant-negative phenotyping\",\n      \"pmids\": [\"22242896\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether antioxidant role reflects PLP directly or downstream PLP-dependent enzymes not separated\", \"Genetic essentiality of PDX1 not tested by knockout\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"To visualize the assembled machine, structural work resolved a dodecameric PDX1 core randomly decorated with up to 12 PfPdx2 subunits, the pentose Schiff base at Lys84, open/closed conformations, and a regulated transient ammonia tunnel, plus fiber organization unique to Plasmodium.\",\n      \"evidence\": \"Cryo-EM, X-ray crystallography, and site-directed mutagenesis of interface methionines\",\n      \"pmids\": [\"22244765\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional significance of the fiber arrangement in vivo unknown\", \"Dynamics of tunnel gating during turnover not directly captured\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"To pursue PDX1 as a drug target, E4P and its hydrazide 4PEHz were shown to inhibit the enzyme and complex, with overexpression protecting parasites, providing in vivo on-target validation.\",\n      \"evidence\": \"In vitro inhibition assays, docking, transgenic overexpression protection, and parasite culture IC50\",\n      \"pmids\": [\"23039077\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whole-cell potency and selectivity of 4PEHz modest\", \"No co-structure of inhibitor bound to PDX1\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"To test conservation of the assembly across species, the P. vivax PDX1 ortholog was shown to form a dodecameric core that assembles with Pdx2 into a monodisperse ring-shaped 24-mer.\",\n      \"evidence\": \"DLS, SAXS, and EM on purified P. vivax Pdx1/Pdx2\",\n      \"pmids\": [\"32825141\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mutagenesis or activity validation of the P. vivax complex\", \"Catalytic parameters for P. vivax PDX1 not measured\"],\n      \"attribution\": [{\"species\": \"Plasmodium vivax\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"To broaden the inhibitor chemical space, DATP 18 was shown to inhibit PDX1 with ~twofold greater in vitro potency than 4PEHz, nominating a new scaffold against the enzyme.\",\n      \"evidence\": \"Single in vitro enzyme inhibition assay\",\n      \"pmids\": [\"36251345\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No in vivo target validation for PDX1 with this compound\", \"Selectivity and whole-parasite activity not established\", \"Binding mode not determined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PDX1 is genetically essential for blood-stage growth by direct gene knockout, and the structural basis of inhibitor binding, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No conditional knockout or genetic essentiality data in the corpus\", \"No inhibitor-bound co-structure of PDX1\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0036381\", \"supporting_discovery_ids\": [0, 1, 3, 5, 7]},\n      {\"term_id\": \"GO:0016765\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"GO:0042803\", \"supporting_discovery_ids\": [3, 4, 7]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0042819\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0008615\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0006979\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"Heteromeric PLP synthase complex (dodecameric PDX1 core + up to 12 PfPdx2 glutaminase subunits, 24-mer)\"\n    ],\n    \"partners\": [\n      \"PfPdx2 (glutaminase subunit)\"\n    ],\n    \"other_free_text\": [\n      \"Pentose substrate ribose 5-phosphate forms a Schiff base at Lys84 of PDX1 [#7]\",\n      \"Interface residues R85/H88/E91 required for dodecamer assembly and PfPdx2 binding; D26/K83/K151 required for catalysis [#3]\",\n      \"G155 flexibility required for hexamer-to-dodecamer transition [#4]; N-terminal \\u03b1N-helix required for complex formation [#2]; C-terminus provides monomer assembly, R5P binding, I320 intermediate formation and trans PLP synthesis [#5]\",\n      \"Inhibited by E4P/4PEHz (substrate analogue, on-target in vivo) [#8] and DATP 18 scaffold [#10]\",\n      \"P. vivax PDX1 ortholog forms an analogous dodecameric core / 24-mer with Pdx2 [#9]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0621200","name":null,"product":"pyridoxine biosynthesis protein PDX1","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1120200","name":null,"product":"pyridoxine biosynthesis protein PDX1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1129000","name":null,"product":"pyridoxine biosynthesis protein PDX1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"PDX1","evaluation":null}