{"gene":"PF3D7_1226300","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2018,"finding":"HAD2 (PF3D7_1226300) was experimentally characterized as a phosphatase belonging to the haloacid dehalogenase-like hydrolase (HAD) superfamily; loss-of-function mutations in HAD2 were identified as necessary for fosmidomycin (FSM) resistance in P. falciparum, establishing HAD2 as a novel regulator of parasite metabolism and drug sensitivity.","method":"Enzymatic characterization (phosphatase activity assay), forward genetic selection of FSM-resistant mutants, metabolic profiling of resistant parasites","journal":"mBio","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — enzymatic activity directly demonstrated in vitro, combined with genetic loss-of-function and metabolic profiling in a single rigorous study","pmids":["30425143"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2018,"finding":"Loss-of-function in HAD2 (PF3D7_1226300) leads to increased steady-state levels of methylerythritol phosphate (MEP) pathway and glycolytic intermediates, indicating that HAD2 phosphatase activity normally constrains flux through these pathways; suppressor mutations in glycolytic enzyme PFK9 restored growth and FSM sensitivity in HAD2-deficient parasites, placing HAD2 genetically upstream of or in parallel with PFK9 in metabolic regulation.","method":"Metabolic profiling of resistant and suppressed strains; forward genetic suppressor screen identifying hypomorphic PFK9 mutations; genetic epistasis analysis","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via suppressor screen combined with metabolic profiling, multiple orthogonal methods in a single rigorous study","pmids":["30425143"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]}],"current_model":"HAD2 (PF3D7_1226300) is a phosphatase of the HAD superfamily that normally constrains steady-state levels of MEP-pathway and glycolytic intermediates in P. falciparum; loss-of-function mutations in HAD2 cause fosmidomycin resistance by elevating these intermediates, and this resistance can be suppressed by hypomorphic mutations in the glycolytic enzyme PFK9, placing HAD2 as a key regulator of metabolic homeostasis and drug sensitivity upstream of or in parallel with PFK9."},"narrative":{"mechanistic_narrative":"HAD2 (PF3D7_1226300) is a phosphatase of the haloacid dehalogenase-like hydrolase superfamily in Plasmodium falciparum that acts as a regulator of central carbon and isoprenoid-precursor metabolism [PMID:30425143]. Its phosphatase activity normally constrains the steady-state levels of methylerythritol phosphate (MEP) pathway and glycolytic intermediates; loss-of-function mutations elevate these metabolites and confer resistance to fosmidomycin, a drug targeting the MEP pathway [PMID:30425143]. Genetically, HAD2 sits upstream of or in parallel with the glycolytic enzyme PFK9: hypomorphic PFK9 mutations suppress the growth defect and restore fosmidomycin sensitivity of HAD2-deficient parasites, placing HAD2 within a metabolic-homeostasis circuit that also governs drug sensitivity [PMID:30425143]. Beyond this phosphatase-and-metabolic-regulation role established in P. falciparum 3D7, no further mechanistic detail — including its direct physiological substrate — has been characterized in the available corpus.","teleology":[{"year":2018,"claim":"Whether any parasite factor could modulate sensitivity to fosmidomycin through metabolism was unknown; identifying HAD2 as a HAD-superfamily phosphatase whose loss confers resistance established a new metabolic node controlling drug sensitivity.","evidence":"In vitro phosphatase assay plus forward genetic selection of fosmidomycin-resistant mutants and metabolic profiling in P. falciparum 3D7","pmids":["30425143"],"confidence":"High","gaps":["The direct physiological substrate of HAD2 is not identified","The structural basis of its phosphatase activity is not resolved","How loss-of-function alleles reduce or abolish activity mechanistically is not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2018,"claim":"It was unclear how HAD2 loss produced resistance; showing that loss elevates MEP-pathway and glycolytic intermediates and that PFK9 hypomorphs suppress the phenotype placed HAD2 in a metabolic-regulatory circuit upstream of or parallel to glycolysis.","evidence":"Metabolic profiling of resistant and suppressed strains plus a forward genetic suppressor screen and epistasis analysis in P. falciparum 3D7","pmids":["30425143"],"confidence":"High","gaps":["Whether HAD2 acts directly on glycolytic/MEP intermediates or through an intermediary is not established","The molecular basis of the genetic interaction between HAD2 and PFK9 is not resolved","Physiological function of HAD2 outside the drug-resistance context is not characterized"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":null,"claim":"The direct enzymatic substrate of HAD2 and the precise mechanism by which it constrains metabolic flux remain unknown.","evidence":"","pmids":[],"confidence":"High","gaps":["No physiological substrate identified in the available corpus","No structural model of HAD2","Subcellular localization of HAD2 is not characterized"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFK9 (GENETIC SUPPRESSOR INTERACTION) [#1]"],"other_free_text":["Loss-of-function mutations in HAD2 confer fosmidomycin resistance in P. falciparum 3D7 [#0].","HAD2 loss elevates steady-state MEP-pathway and glycolytic intermediates, indicating a flux-constraining regulatory role [#1]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"30425143","id":"PMC_30425143","title":"Suppression of Drug Resistance Reveals a Genetic Mechanism of Metabolic Plasticity in Malaria Parasites.","date":"2018","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/30425143","citation_count":22,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["HAD2","haloacid dehalogenase-like hydrolase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31205418","id":"PMC_31205418","title":"Haloacid Dehalogenase Proteins: Novel Mediators of Metabolic Plasticity in Plasmodium falciparum.","date":"2019","source":"Microbiology insights","url":"https://pubmed.ncbi.nlm.nih.gov/31205418","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["HAD2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32593550","id":"PMC_32593550","title":"A computational approach to validate novel drug targets of gentianine from Swertiya chirayita in Plasmodium falciparum.","date":"2020","source":"Bio Systems","url":"https://pubmed.ncbi.nlm.nih.gov/32593550","citation_count":3,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["haloacid dehalogenase-like hydrolase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4294,"output_tokens":727,"usd":0.011893,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5426,"output_tokens":1621,"usd":0.033828,"stage2_stop_reason":"end_turn"},"total_usd":0.045721,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"HAD2 (PF3D7_1226300) was experimentally characterized as a phosphatase belonging to the haloacid dehalogenase-like hydrolase (HAD) superfamily; loss-of-function mutations in HAD2 were identified as necessary for fosmidomycin (FSM) resistance in P. falciparum, establishing HAD2 as a novel regulator of parasite metabolism and drug sensitivity.\",\n      \"method\": \"Enzymatic characterization (phosphatase activity assay), forward genetic selection of FSM-resistant mutants, metabolic profiling of resistant parasites\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — enzymatic activity directly demonstrated in vitro, combined with genetic loss-of-function and metabolic profiling in a single rigorous study\",\n      \"pmids\": [\"30425143\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Loss-of-function in HAD2 (PF3D7_1226300) leads to increased steady-state levels of methylerythritol phosphate (MEP) pathway and glycolytic intermediates, indicating that HAD2 phosphatase activity normally constrains flux through these pathways; suppressor mutations in glycolytic enzyme PFK9 restored growth and FSM sensitivity in HAD2-deficient parasites, placing HAD2 genetically upstream of or in parallel with PFK9 in metabolic regulation.\",\n      \"method\": \"Metabolic profiling of resistant and suppressed strains; forward genetic suppressor screen identifying hypomorphic PFK9 mutations; genetic epistasis analysis\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via suppressor screen combined with metabolic profiling, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"30425143\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}\n      ]\n    }\n  ],\n  \"current_model\": \"HAD2 (PF3D7_1226300) is a phosphatase of the HAD superfamily that normally constrains steady-state levels of MEP-pathway and glycolytic intermediates in P. falciparum; loss-of-function mutations in HAD2 cause fosmidomycin resistance by elevating these intermediates, and this resistance can be suppressed by hypomorphic mutations in the glycolytic enzyme PFK9, placing HAD2 as a key regulator of metabolic homeostasis and drug sensitivity upstream of or in parallel with PFK9.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HAD2 (PF3D7_1226300) is a phosphatase of the haloacid dehalogenase-like hydrolase superfamily in Plasmodium falciparum that acts as a regulator of central carbon and isoprenoid-precursor metabolism [#0]. Its phosphatase activity normally constrains the steady-state levels of methylerythritol phosphate (MEP) pathway and glycolytic intermediates; loss-of-function mutations elevate these metabolites and confer resistance to fosmidomycin, a drug targeting the MEP pathway [#0, #1]. Genetically, HAD2 sits upstream of or in parallel with the glycolytic enzyme PFK9: hypomorphic PFK9 mutations suppress the growth defect and restore fosmidomycin sensitivity of HAD2-deficient parasites, placing HAD2 within a metabolic-homeostasis circuit that also governs drug sensitivity [#1]. Beyond this phosphatase-and-metabolic-regulation role established in P. falciparum 3D7, no further mechanistic detail — including its direct physiological substrate — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether any parasite factor could modulate sensitivity to fosmidomycin through metabolism was unknown; identifying HAD2 as a HAD-superfamily phosphatase whose loss confers resistance established a new metabolic node controlling drug sensitivity.\",\n      \"evidence\": \"In vitro phosphatase assay plus forward genetic selection of fosmidomycin-resistant mutants and metabolic profiling in P. falciparum 3D7\",\n      \"pmids\": [\"30425143\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The direct physiological substrate of HAD2 is not identified\",\n        \"The structural basis of its phosphatase activity is not resolved\",\n        \"How loss-of-function alleles reduce or abolish activity mechanistically is not defined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"It was unclear how HAD2 loss produced resistance; showing that loss elevates MEP-pathway and glycolytic intermediates and that PFK9 hypomorphs suppress the phenotype placed HAD2 in a metabolic-regulatory circuit upstream of or parallel to glycolysis.\",\n      \"evidence\": \"Metabolic profiling of resistant and suppressed strains plus a forward genetic suppressor screen and epistasis analysis in P. falciparum 3D7\",\n      \"pmids\": [\"30425143\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether HAD2 acts directly on glycolytic/MEP intermediates or through an intermediary is not established\",\n        \"The molecular basis of the genetic interaction between HAD2 and PFK9 is not resolved\",\n        \"Physiological function of HAD2 outside the drug-resistance context is not characterized\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct enzymatic substrate of HAD2 and the precise mechanism by which it constrains metabolic flux remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No physiological substrate identified in the available corpus\",\n        \"No structural model of HAD2\",\n        \"Subcellular localization of HAD2 is not characterized\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016791\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0019288\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0006096\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PFK9 (genetic suppressor interaction) [#1]\"\n    ],\n    \"other_free_text\": [\n      \"Loss-of-function mutations in HAD2 confer fosmidomycin resistance in P. falciparum 3D7 [#0].\",\n      \"HAD2 loss elevates steady-state MEP-pathway and glycolytic intermediates, indicating a flux-constraining regulatory role [#1].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1226300","name":null,"product":"haloacid dehalogenase-like hydrolase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1441100","name":null,"product":"haloacid dehalogenase-like hydrolase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1445700","name":null,"product":"haloacid dehalogenase-like hydrolase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"HAD2","evaluation":null}