{"id":"bbb25e1d-9704-5d62-be8b-1aa74d4599d6","stable_key":"548ab9d6-3a9b-5bed-879c-17d03813b636:b2-pdxk-pyridoxal-route","predicate":"phosphorylates","statement":"Human PDXK assays directly measured ATP-dependent conversion of pyridoxal to PLP, a reaction distinct from PNPO oxidation.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"positive","is_public":true,"mechanism_event_id":"471c879b-a313-5e61-bfae-8199b9316209","mechanism_event_label":"Not every route to active B6 passes through PNPO.","subject":{"id":"d2d46db7-13a4-595f-adaa-70ad6ca31a6c","slug":"pdxk","display_name":"Pyridoxal kinase / PDXK","entity_type_key":"protein"},"object":{"id":"9bf6269d-9e01-553d-bd8b-11a0d613bfca","slug":"pyridoxal","display_name":"Pyridoxal","entity_type_key":"small_molecule"},"evidence_count":1,"mechanism_event":{"id":"471c879b-a313-5e61-bfae-8199b9316209","stable_key":"548ab9d6-3a9b-5bed-879c-17d03813b636:b2-pdxk-pyridoxal-route-event","event_type":"biochemical_relationship","label":"Not every route to active B6 passes through PNPO.","description":"Human PDXK assays directly measured ATP-dependent conversion of pyridoxal to PLP, a reaction distinct from PNPO oxidation.","status":"provisional","compartment":null,"participants":[{"entity":{"id":"9bf6269d-9e01-553d-bd8b-11a0d613bfca","slug":"pyridoxal","display_name":"Pyridoxal","entity_type_key":"small_molecule"},"role":"substrate","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"58b974f1-d389-5bf6-81cd-889c44442c42","slug":"atp","display_name":"ATP","entity_type_key":"small_molecule"},"role":"phosphate donor","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"6b656ff5-9532-5da4-8eea-8ca163a48649","slug":"pyridoxal-phosphate","display_name":"PLP","entity_type_key":"small_molecule"},"role":"product","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"bff427ab-35f9-59c2-bb24-fd5953bbaec2","slug":"magnesium-ion","display_name":"Mg2+","entity_type_key":"ion"},"role":"assay MgATP cofactor","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"d2d46db7-13a4-595f-adaa-70ad6ca31a6c","slug":"pdxk","display_name":"Pyridoxal kinase / PDXK","entity_type_key":"protein"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""}]},"contexts":[{"dimension":"cross_nutrient","value_text":"Separates the B6 phosphorylation step from the B2-dependent oxidation step.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"evidence_location","value_text":"Abstract","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Recombinant human PDXK expressed in E. coli; PL-to-PLP kinetics and unliganded/MgATP-bound structures.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"exposure","value_text":"Purified-enzyme assay","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"This biochemical route does not establish that dietary pyridoxal bypasses all consequences of PNPO disease.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"Riboflavin research collection; topical membership is not evidence of a direct dietary effect.","comparator":null,"unit":null,"notes":"","entity":{"slug":"riboflavin","display_name":"Riboflavin (vitamin B2)","entity_type_key":"small_molecule"}},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"Not every route to active B6 passes through PNPO.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[safo2007] Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. (2007). https://pubmed.ncbi.nlm.nih.gov/17766369/ DOI: 10.1110/ps.073022107","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Purified recombinant enzyme; no intact tissue","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"1909a518-56a3-5839-bc7e-b29a1e30c073","evidence_kind":"source_excerpt","locator":"Lines 1192-1204","start_line":1192,"end_line":1204,"excerpt":"### b2-pdxk-pyridoxal-route\nHuman PDXK assays directly measured ATP-dependent conversion of pyridoxal to PLP, a reaction distinct from PNPO oxidation.\nCondition category: normal\nnutrient_topic: Riboflavin research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: Not every route to active B6 passes through PNPO.\norganism: Homo sapiens\ntissue_or_cell_type: Purified recombinant enzyme; no intact tissue\nexperimental_model: Recombinant human PDXK expressed in E. coli; PL-to-PLP kinetics and unliganded/MgATP-bound structures.\nlimitations: This biochemical route does not establish that dietary pyridoxal bypasses all consequences of PNPO disease.\nexposure: Purified-enzyme assay\ncross_nutrient: Separates the B6 phosphorylation step from the B2-dependent oxidation step.\nevidence_location: Abstract\n[safo2007] Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. 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