{"id":"3427bfa6-9977-51ea-9c35-2934b78a651e","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:lysine-adenylation","predicate":"converted_to","statement":"KARS1 activates lysine with ATP, forming enzyme-bound lysyl-adenylate and releasing pyrophosphate.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"0014be8d-8c8d-5d32-827c-4bf22924c565","mechanism_event_label":"ATP activates lysine before it is attached to its carrier RNA.","subject":{"id":"5fff6664-209e-5c35-b88e-ac15c1c5fbc0","slug":"l-lysine","display_name":"L-Lysine","entity_type_key":"small_molecule"},"object":{"id":"a812ec0c-6962-580b-bf08-5e7c74b7b5ba","slug":"lysyl-adenylate","display_name":"Lysyl-adenylate","entity_type_key":"small_molecule"},"evidence_count":1,"mechanism_event":{"id":"0014be8d-8c8d-5d32-827c-4bf22924c565","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:lysine-adenylation-event","event_type":"biochemical_relationship","label":"ATP activates lysine before it is attached to its carrier RNA.","description":"KARS1 activates lysine with ATP, forming enzyme-bound lysyl-adenylate and releasing pyrophosphate.","status":"provisional","compartment":{"slug":"cytosol","display_name":"Cytosol"},"participants":[{"entity":{"id":"5764a3e5-0715-5aa3-8c20-c0efb52123b5","slug":"kars1","display_name":"Lysyl-tRNA synthetase / KARS1","entity_type_key":"protein"},"role":"catalyst","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"5fff6664-209e-5c35-b88e-ac15c1c5fbc0","slug":"l-lysine","display_name":"L-Lysine","entity_type_key":"small_molecule"},"role":"substrate","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"58b974f1-d389-5bf6-81cd-889c44442c42","slug":"atp","display_name":"ATP","entity_type_key":"small_molecule"},"role":"cosubstrate","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"a812ec0c-6962-580b-bf08-5e7c74b7b5ba","slug":"lysyl-adenylate","display_name":"Lysyl-adenylate","entity_type_key":"small_molecule"},"role":"intermediate","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"cd026fef-529f-5e03-b6b5-37ede8ce9127","slug":"pyrophosphate","display_name":"Inorganic pyrophosphate","entity_type_key":"small_molecule"},"role":"product","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""}]},"contexts":[{"dimension":"experimental_model","value_text":"Human LysRS cryo-EM and aminoacylation assays","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"The structural experiment used tRNA-Lys3; KARS1 is not the leucyl-tRNA synthetase LARS1.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"ATP activates lysine before it is attached to its carrier RNA.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[devarkar2025] Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase (2025). https://pubmed.ncbi.nlm.nih.gov/40036503/ DOI: 10.1093/nar/gkaf114","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Cytosolic tRNA charging","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"2d2823a8-62dc-57c4-8e80-4b056c31aad1","evidence_kind":"source_excerpt","locator":"Lines 54-62","start_line":54,"end_line":62,"excerpt":"### lysine-adenylation\nKARS1 activates lysine with ATP, forming enzyme-bound lysyl-adenylate and releasing pyrophosphate.\nPlain language: ATP activates lysine before it is attached to its carrier RNA.\nCondition category: normal\norganism: Homo sapiens\ntissue_or_cell_type: Cytosolic tRNA charging\nexperimental_model: Human LysRS cryo-EM and aminoacylation assays\nlimitations: The structural experiment used tRNA-Lys3; KARS1 is not the leucyl-tRNA synthetase LARS1.\n[devarkar2025] Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase (2025). https://pubmed.ncbi.nlm.nih.gov/40036503/ DOI: 10.1093/nar/gkaf114","model_system":"Human LysRS cryo-EM and aminoacylation assays","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact quote from the accompanying curation document, not from publisher text. Original study references: [devarkar2025] Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase (2025). https://pubmed.ncbi.nlm.nih.gov/40036503/ DOI: 10.1093/nar/gkaf114","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}