{"id":"2ff07f1c-9da7-5189-9044-d84a48f8a122","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:ribosomal-lysine-incorporation","predicate":"incorporated_into","statement":"At the cytosolic 80S ribosome, the alpha-amino group of A-site lysyl-tRNA accepts the P-site nascent peptide, incorporating lysine into a peptide bond; the extended chain remains attached to the incoming tRNA.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"e1488ea2-1e14-57d0-8f17-7172963c6647","mechanism_event_label":"The ribosome adds charged lysine to a growing protein chain.","subject":{"id":"165668b6-4ca7-5558-aabb-506ae43314e7","slug":"lysyl-trna-lys","display_name":"Lysyl-tRNA-Lys","entity_type_key":"rna"},"object":{"id":"44399a64-dd8a-5818-a863-b3389c6adf37","slug":"protein-bound-lysine","display_name":"Protein-bound lysine residue","entity_type_key":"protein_state"},"evidence_count":1,"mechanism_event":{"id":"e1488ea2-1e14-57d0-8f17-7172963c6647","stable_key":"c3df3634-4c3a-5099-a5d9-e4f6344c1084:ribosomal-lysine-incorporation-event","event_type":"biochemical_relationship","label":"The ribosome adds charged lysine to a growing protein chain.","description":"At the cytosolic 80S ribosome, the alpha-amino group of A-site lysyl-tRNA accepts the P-site nascent peptide, incorporating lysine into a peptide bond; the extended chain remains attached to the incoming tRNA.","status":"provisional","compartment":{"slug":"cytosol","display_name":"Cytosol"},"participants":[{"entity":{"id":"a55c1d91-46f1-5f02-8111-0032c7c78192","slug":"cytosolic-80s-ribosome","display_name":"Cytosolic 80S ribosome","entity_type_key":"protein_complex"},"role":"catalyst","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"165668b6-4ca7-5558-aabb-506ae43314e7","slug":"lysyl-trna-lys","display_name":"Lysyl-tRNA-Lys","entity_type_key":"rna"},"role":"substrate","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"cba99e3e-5655-5745-8bbf-7cbf0bd226a9","slug":"peptidyl-trna","display_name":"P-site peptidyl-tRNA","entity_type_key":"rna"},"role":"peptide_donor","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"a73648d6-902e-5e98-bc8e-16d8772bd166","slug":"lysine-codon-mrna","display_name":"mRNA carrying a lysine codon","entity_type_key":"rna"},"role":"template","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"c4db3b56-a474-5a8b-a8b3-9dc9f1568aa0","slug":"lysine-extended-peptidyl-trna","display_name":"Lysine-extended peptidyl-tRNA","entity_type_key":"rna"},"role":"product","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""},{"entity":{"id":"44399a64-dd8a-5818-a863-b3389c6adf37","slug":"protein-bound-lysine","display_name":"Protein-bound lysine residue","entity_type_key":"protein_state"},"role":"incorporated_residue","stoichiometry":null,"state_label":"","sequence_order":5,"notes":""}]},"contexts":[{"dimension":"experimental_model","value_text":"Human cell lysate translation products; rabbit reticulocyte ribosome-nascent-chain cryo-EM","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"AAG-coded translation controls directly show elongation. The structural experiment concerns poly(A)-dependent stalling; it does not establish a dietary deficiency response or instant release of the lysine-carrying tRNA.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Homo sapiens and Oryctolagus cuniculus","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"The ribosome adds charged lysine to a growing protein chain.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[chandrasekaran2019] Mechanism of ribosome stalling during translation of a poly(A) tail (2019). https://pmc.ncbi.nlm.nih.gov/articles/PMC6900289/ DOI: 10.1038/s41594-019-0331-x","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Cytosolic translation; cultured-cell lysate and reticulocyte lysate","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"732f12a7-d558-5920-a4bf-5d29a18f2a23","evidence_kind":"source_excerpt","locator":"Lines 347-355","start_line":347,"end_line":355,"excerpt":"### ribosomal-lysine-incorporation\nAt the cytosolic 80S ribosome, the alpha-amino group of A-site lysyl-tRNA accepts the P-site nascent peptide, incorporating lysine into a peptide bond; the extended chain remains attached to the incoming tRNA.\nPlain language: The ribosome adds charged lysine to a growing protein chain.\nCondition category: normal\norganism: Homo sapiens and Oryctolagus cuniculus\ntissue_or_cell_type: Cytosolic translation; cultured-cell lysate and reticulocyte lysate\nexperimental_model: Human cell lysate translation products; rabbit reticulocyte ribosome-nascent-chain cryo-EM\nlimitations: AAG-coded translation controls directly show elongation. The structural experiment concerns poly(A)-dependent stalling; it does not establish a dietary deficiency response or instant release of the lysine-carrying tRNA.\n[chandrasekaran2019] Mechanism of ribosome stalling during translation of a poly(A) tail (2019). https://pmc.ncbi.nlm.nih.gov/articles/PMC6900289/ DOI: 10.1038/s41594-019-0331-x","model_system":"Human cell lysate translation products; rabbit reticulocyte ribosome-nascent-chain cryo-EM","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact quote from the accompanying curation document, not from publisher text. Original study references: [chandrasekaran2019] Mechanism of ribosome stalling during translation of a poly(A) tail (2019). https://pmc.ncbi.nlm.nih.gov/articles/PMC6900289/ DOI: 10.1038/s41594-019-0331-x","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}