{"id":"87f077e6-9a7d-5762-b7d3-f435563cd157","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:plod3-collagen-hydroxylation","predicate":"hydroxylates","statement":"PLOD3 hydroxylates peptidyl lysine using Fe(II), 2-oxoglutarate and oxygen.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"bcbc93a5-9e7b-5192-8fbd-e361feb4a6a0","mechanism_event_label":"The collagen enzyme needs an iron-containing catalytic site and reaction partners.","subject":{"id":"2b488aa8-b4d8-5d2e-bb4c-03047e3e030f","slug":"plod3","display_name":"PLOD3","entity_type_key":"protein"},"object":{"id":"34b151b4-591b-5008-bc84-5f1d610d102b","slug":"collagen-lysine-residues","display_name":"Collagen-bound lysine residues","entity_type_key":"protein_state"},"evidence_count":1,"mechanism_event":{"id":"bcbc93a5-9e7b-5192-8fbd-e361feb4a6a0","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:plod3-collagen-hydroxylation-event","event_type":"biochemical_relationship","label":"The collagen enzyme needs an iron-containing catalytic site and reaction partners.","description":"PLOD3 hydroxylates peptidyl lysine using Fe(II), 2-oxoglutarate and oxygen.","status":"provisional","compartment":{"slug":"endoplasmic-reticulum","display_name":"Endoplasmic reticulum"},"participants":[{"entity":{"id":"2b488aa8-b4d8-5d2e-bb4c-03047e3e030f","slug":"plod3","display_name":"PLOD3","entity_type_key":"protein"},"role":"enzyme","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"34b151b4-591b-5008-bc84-5f1d610d102b","slug":"collagen-lysine-residues","display_name":"Collagen-bound lysine residues","entity_type_key":"protein_state"},"role":"substrate","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"7c465ab2-233e-5401-9706-3492e9ea8f45","slug":"collagen-hydroxylysine-residues","display_name":"Collagen-bound 5-hydroxylysine residues","entity_type_key":"protein_state"},"role":"product","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"59d6d1cd-df32-5b58-b950-3188bc7b95d6","slug":"iron-ii","display_name":"Ferrous iron","entity_type_key":"ion"},"role":"cofactor","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"628ddc2d-e4d9-59c7-ae76-0c0cab80a6b1","slug":"2-oxoglutarate","display_name":"2-Oxoglutarate","entity_type_key":"small_molecule"},"role":"cosubstrate","stoichiometry":null,"state_label":"","sequence_order":4,"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":5,"notes":""},{"entity":{"id":"38d0c4d9-53d1-5239-bfe3-c1b5e9b79085","slug":"ascorbate","display_name":"L-Ascorbate","entity_type_key":"small_molecule"},"role":"supporting_reductant","stoichiometry":null,"state_label":"","sequence_order":6,"notes":""},{"entity":{"id":"462f63ce-a2c1-5312-9c14-70b8b12e1d6e","slug":"succinate","display_name":"Succinate","entity_type_key":"small_molecule"},"role":"coproduct","stoichiometry":null,"state_label":"","sequence_order":7,"notes":""},{"entity":{"id":"966f14e5-c82f-5535-ad89-bfcc0adb2232","slug":"carbon-dioxide","display_name":"Carbon dioxide","entity_type_key":"small_molecule"},"role":"coproduct","stoichiometry":null,"state_label":"","sequence_order":8,"notes":""}]},"contexts":[{"dimension":"experimental_model","value_text":"Recombinant human PLOD3 structural and biochemical assays.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"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":"The collagen enzyme needs an iron-containing catalytic site and reaction partners.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[plod3-2018] Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 (2018). https://www.nature.com/articles/s41467-018-05631-5 DOI: 10.1038/s41467-018-05631-5","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":"e24da071-a4db-59c8-ac0c-5e4b9ed3fc09","evidence_kind":"source_excerpt","locator":"Lines 417-425","start_line":417,"end_line":425,"excerpt":"### plod3-collagen-hydroxylation\nPLOD3 hydroxylates peptidyl lysine using Fe(II), 2-oxoglutarate and oxygen.\nPlain language: The collagen enzyme needs an iron-containing catalytic site and reaction partners.\nCondition category: normal\norganism: Human\ntissue_or_cell_type: Not specified as a whole tissue; see experimental model.\nexperimental_model: Recombinant human PLOD3 structural and biochemical assays.\nlimitations: 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[plod3-2018] Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 (2018). https://www.nature.com/articles/s41467-018-05631-5 DOI: 10.1038/s41467-018-05631-5","model_system":"Recombinant human PLOD3 structural and biochemical assays.","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact quote from the accompanying curation document, not from publisher text. Original study references: [plod3-2018] Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 (2018). https://www.nature.com/articles/s41467-018-05631-5 DOI: 10.1038/s41467-018-05631-5","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}