{"id":"af6e2958-5121-5fec-beed-bc1474d14696","stable_key":"research:sepsecs-chemistry","predicate":"catalyzes_formation_of","statement":"PLP-dependent SEPSECS converts phosphoseryl-tRNA Sec to Sec-tRNA through phosphate elimination and selenium donation from selenophosphate, not incorporation of intact selenophosphate.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"literature_reviewed:direct_experimental","direction":"positive","is_public":true,"mechanism_event_id":"86e8483f-1a28-5b1d-a432-651bada0f672","mechanism_event_label":"SEPSECS uses selenium from the donor to finish the tRNA-bound amino acid.","subject":{"id":"192979cc-02fb-5913-bace-5d5ba3983f51","slug":"sepsecs","display_name":"SEPSECS / SepSecS","entity_type_key":"protein"},"object":{"id":"15ce9978-f9e2-528c-8a2f-1079154b5383","slug":"sec-trna","display_name":"Sec-tRNA[Ser]Sec","entity_type_key":"rna"},"evidence_count":1,"mechanism_event":{"id":"86e8483f-1a28-5b1d-a432-651bada0f672","stable_key":"research:sepsecs-chemistry","event_type":"catalysis","label":"SEPSECS uses selenium from the donor to finish the tRNA-bound amino acid.","description":"PLP-dependent SEPSECS converts phosphoseryl-tRNA Sec to Sec-tRNA through phosphate elimination and selenium donation from selenophosphate, not incorporation of intact selenophosphate.","status":"active","compartment":null,"participants":[{"entity":{"id":"5b2eb213-ab47-5a57-871a-e00a5ef02990","slug":"phosphoseryl-trna-sec","display_name":"O-phosphoseryl-tRNA Sec","entity_type_key":"rna"},"role":"substrate","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"f997135c-327f-5eb7-b159-1f046d14d4c2","slug":"selenophosphate","display_name":"Selenophosphate","entity_type_key":"chemical_species"},"role":"selenium_donor","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"192979cc-02fb-5913-bace-5d5ba3983f51","slug":"sepsecs","display_name":"SEPSECS / SepSecS","entity_type_key":"protein"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"15ce9978-f9e2-528c-8a2f-1079154b5383","slug":"sec-trna","display_name":"Sec-tRNA[Ser]Sec","entity_type_key":"rna"},"role":"object","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""}]},"contexts":[{"dimension":"cell_type","value_text":"Purified enzyme/tRNA","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Human enzyme/tRNA crystallography and biochemical assays","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Not a measurement of dietary intake effects.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"2dc048a4-faa7-5aa3-9dc2-5cd916ec3dc1","evidence_kind":"curated_literature_summary","locator":"lines 1154-1164","start_line":1154,"end_line":1164,"excerpt":"## sepsecs-chemistry\n\nSEPSECS uses selenium from the donor to finish the tRNA-bound amino acid.\n\nPLP-dependent SEPSECS converts phosphoseryl-tRNA Sec to Sec-tRNA through phosphate elimination and selenium donation from selenophosphate, not incorporation of intact selenophosphate.\n\nOrganism: Homo sapiens\nCell type: Purified enzyme/tRNA\nExperimental model: Human enzyme/tRNA crystallography and biochemical assays\nLimitations: Not a measurement of dietary intake effects.\nPrimary reference: [The human SepSecS–tRNASec complex reveals mechanism of selenocysteine formation](https://pubmed.ncbi.nlm.nih.gov/19608919/)","model_system":"Human enzyme/tRNA crystallography and biochemical assays","directness":"author_interpretation","verification_status":"secondary_verified","notes":"Curated summary; inspect the linked primary papers for original methods and results.","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"4f892f13-06ea-5199-a33c-a703f35c80ae","stable_key":"selenium-research-2026-09-17","title":"Selenium: literature corrections and mechanism additions","document_type":"curated_literature_review","citation_label":"Metabolic Ledger literature curation, 17 September 2026; primary papers linked individually","file_path":"","sha256":"0b818b10c1c7120e5caf7f4d4019d7bd025d745692e424f515d3ef903c9ab7f3","revision_id":"80984e03-5f0f-5877-8094-afef7637444e","review_status":"secondary_verified","notes":"Secondary curated summaries of primary experiments, with explicit models and limitations. Not archived primary full text."}}],"relations":[],"conflicts":[],"corrections":[{"id":"2c57c4ac-75e2-5d18-81f0-09bcb5ededde","title":"SEPSECS uses selenium from selenophosphate, not intact selenophosphate substitution","kind":"contradiction","status":"corrected","why":"The phosphate-for-selenophosphate wording gives the wrong product. SerRS charging is an obligatory precursor step, not an aminoacylation error.","resolution":"Record phosphate elimination/selenium donation; retain the later correction of the mischarging interpretation.","created_at":"2026-09-17 07:19:34","record_type":"correction","display_label":"Correction history","record_url":"/corrections/2c57c4ac-75e2-5d18-81f0-09bcb5ededde","literature_review":{"revision_id":"80984e03-5f0f-5877-8094-afef7637444e","start_line":1511,"end_line":1516,"papers":[{"paper_key":"palioura-2009","title":"The human SepSecS–tRNASec complex reveals mechanism of selenocysteine formation","url":"https://pubmed.ncbi.nlm.nih.gov/19608919/","doi":"10.1126/science.1173755","year":2009,"model":"Human enzyme/tRNA crystallography and biochemical assays","summary":"Selenophosphate supplies selenium rather than being incorporated intact."}]},"sides":[{"conflict_id":"2c57c4ac-75e2-5d18-81f0-09bcb5ededde","ordinal":0,"label":"Original preserved statement","revision_id":"1fa1ebde-141f-5d47-8a4f-ba87ff84a6c6","start_line":16,"end_line":18,"quote":"3. **SerRS** mischarges tRNA^[Ser]Sec with plain **serine**. Wrong amino acid, on purpose.\n4. **PSTK** phosphorylates it → **O-phosphoseryl-tRNA**.\n5. **SepSecS** swaps the phosphate for selenophosphate → **Sec-tRNA^[Ser]Sec**. (Fun aside: SepSecS is the SLA/LP autoantigen in autoimmune hepatitis. Your immune system attacking the selenium machine.)","claim_id":null,"source_key":"molecular","source_title":"Selenium: the molecular cascade","claim_ids":[]},{"conflict_id":"2c57c4ac-75e2-5d18-81f0-09bcb5ededde","ordinal":1,"label":"Original preserved statement","revision_id":"f8f97804-c1fb-56df-9c06-c02e36e2a5b8","start_line":43,"end_line":43,"quote":"SerRS charging tRNA^[Ser]Sec with serine is an obligatory biosynthetic step, not a mistake. SEPHS2 supplies selenophosphate, while PSTK and SEPSECS convert the serine-charged tRNA into Sec-tRNA^[Ser]Sec.","claim_id":null,"source_key":"deficiency","source_title":"Selenium deficiency: a mechanism-first reference","claim_ids":[]},{"conflict_id":"2c57c4ac-75e2-5d18-81f0-09bcb5ededde","ordinal":2,"label":"Literature correction and experimental limits","revision_id":"80984e03-5f0f-5877-8094-afef7637444e","start_line":1511,"end_line":1516,"quote":"## SEPSECS uses selenium from selenophosphate, not intact selenophosphate substitution\n\nThe phosphate-for-selenophosphate wording gives the wrong product. SerRS charging is an obligatory precursor step, not an aminoacylation error.\n\nRecord phosphate elimination/selenium donation; retain the later correction of the mischarging interpretation.\nPrimary reference: [The human SepSecS–tRNASec complex reveals mechanism of selenocysteine formation](https://pubmed.ncbi.nlm.nih.gov/19608919/)","claim_id":null,"source_key":"selenium-research-2026-09-17","source_title":"Selenium: literature corrections and mechanism additions","claim_ids":[]}]}],"research":{"topic":"Selenium scientific audit","plain_language":"SEPSECS uses selenium from the donor to finish the tRNA-bound amino acid.","evidence_scope":"direct_experimental","papers":[{"key":"palioura-2009","title":"The human SepSecS–tRNASec complex reveals mechanism of selenocysteine formation","url":"https://pubmed.ncbi.nlm.nih.gov/19608919/","doi":"10.1126/science.1173755","year":2009,"model":"Human enzyme/tRNA crystallography and biochemical assays","summary":"Selenophosphate supplies selenium rather than being incorporated intact."}]}}