{"id":"3e7b8d95-5e5d-5850-a5e8-92f79f196fe9","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:kdm1a-h3k4-demethylation","predicate":"demethylates","statement":"KDM1A/LSD1 oxidatively removes a methyl group from H3K4me2 through a flavin-dependent reaction.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"60477d37-7a16-586f-8c05-098ae23760a9","mechanism_event_label":"Some lysine methyl marks can be erased by a flavin enzyme.","subject":{"id":"05375599-0d5f-5fca-8df5-1c38a3012788","slug":"kdm1a","display_name":"KDM1A","entity_type_key":"protein"},"object":{"id":"bb399b44-2151-5c3f-8bab-30397c494237","slug":"h3k4me2","display_name":"Histone H3 dimethylated at K4","entity_type_key":"protein_state"},"evidence_count":1,"mechanism_event":{"id":"60477d37-7a16-586f-8c05-098ae23760a9","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:kdm1a-h3k4-demethylation-event","event_type":"biochemical_relationship","label":"Some lysine methyl marks can be erased by a flavin enzyme.","description":"KDM1A/LSD1 oxidatively removes a methyl group from H3K4me2 through a flavin-dependent reaction.","status":"provisional","compartment":{"slug":"nucleus","display_name":"Nucleus"},"participants":[{"entity":{"id":"05375599-0d5f-5fca-8df5-1c38a3012788","slug":"kdm1a","display_name":"KDM1A","entity_type_key":"protein"},"role":"enzyme","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"bb399b44-2151-5c3f-8bab-30397c494237","slug":"h3k4me2","display_name":"Histone H3 dimethylated at K4","entity_type_key":"protein_state"},"role":"substrate","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"37c0f163-3aee-5f82-857e-e083c2dbc425","slug":"h3k4me1","display_name":"Histone H3 monomethylated at K4","entity_type_key":"protein_state"},"role":"product","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"e2cd7179-f218-54e8-9ce9-7a836ae35fac","slug":"fad","display_name":"FAD","entity_type_key":"small_molecule"},"role":"cofactor","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"899c7ab0-6f81-5b38-a6bd-fbb33d66ac8d","slug":"oxygen","display_name":"Molecular oxygen","entity_type_key":"small_molecule"},"role":"cosubstrate","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""},{"entity":{"id":"528300c2-5f81-5188-b14c-eafc747cd15b","slug":"formaldehyde","display_name":"Formaldehyde","entity_type_key":"small_molecule"},"role":"coproduct","stoichiometry":null,"state_label":"","sequence_order":5,"notes":""}]},"contexts":[{"dimension":"experimental_model","value_text":"Purified LSD1 enzyme / histone assays and cellular RNA interference.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Do not extend this specific activity to trimethyllysine or every histone site. This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Human","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"Some lysine methyl marks can be erased by a flavin enzyme.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[lsd1-2004] Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 (2004). https://pubmed.ncbi.nlm.nih.gov/15620353/ DOI: 10.1016/j.cell.2004.12.012","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Not specified as a whole tissue; see experimental model.","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"c7f81c69-0849-5e59-a202-e1741cf37577","evidence_kind":"source_excerpt","locator":"Lines 557-565","start_line":557,"end_line":565,"excerpt":"### kdm1a-h3k4-demethylation\nKDM1A/LSD1 oxidatively removes a methyl group from H3K4me2 through a flavin-dependent reaction.\nPlain language: Some lysine methyl marks can be erased by a flavin enzyme.\nCondition category: normal\norganism: Human\ntissue_or_cell_type: Not specified as a whole tissue; see experimental model.\nexperimental_model: Purified LSD1 enzyme / histone assays and cellular RNA interference.\nlimitations: Do not extend this specific activity to trimethyllysine or every histone site. This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome.\n[lsd1-2004] Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 (2004). https://pubmed.ncbi.nlm.nih.gov/15620353/ DOI: 10.1016/j.cell.2004.12.012","model_system":"Purified LSD1 enzyme / histone assays and cellular RNA interference.","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact quote from the accompanying curation document, not from publisher text. Original study references: [lsd1-2004] Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 (2004). https://pubmed.ncbi.nlm.nih.gov/15620353/ DOI: 10.1016/j.cell.2004.12.012","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"7633bde7-dcc9-5086-91c6-a45eb96857f3","stable_key":"import-c3df3634-4c3a-5099-a5d9-e4f6344c1084","title":"L-Lysine: mechanism-first literature curation (2026-09-17)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text.","file_path":"","sha256":"93998d47c21525409ba82f1c82ededf2893dff15fbe61c7deffc175b0e298e97","revision_id":"3897e31f-6624-59e1-a053-8a81b7361632","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[],"corrections":[],"research":null}