{"id":"965bed02-f18f-5b17-8a35-2daac2586bfc","stable_key":"research:ahpc-low-pka","predicate":"exhibits","statement":"Purified bacterial AhpC catalytic cysteine has a measured pKa near 5.9, below the free-cysteine value generalized in the source.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"literature_reviewed:direct_experimental","direction":"neutral","is_public":true,"mechanism_event_id":"615cf1f4-86f1-5f3f-a2e0-ce41153657a3","mechanism_event_label":"An enzyme environment can make cysteine reactive near physiological pH.","subject":{"id":"46e12ef9-2b67-5b52-8af9-59ce78c699f7","slug":"ahpc","display_name":"AhpC","entity_type_key":"protein"},"object":{"id":"fad2ed93-43ff-5630-a150-69416b918bf7","slug":"catalytic-cysteine-ionization","display_name":"catalytic cysteine ionization","entity_type_key":"cellular_process"},"evidence_count":1,"mechanism_event":{"id":"615cf1f4-86f1-5f3f-a2e0-ce41153657a3","stable_key":"research:ahpc-low-pka","event_type":"contextual_mechanism","label":"An enzyme environment can make cysteine reactive near physiological pH.","description":"Purified bacterial AhpC catalytic cysteine has a measured pKa near 5.9, below the free-cysteine value generalized in the source.","status":"active","compartment":null,"participants":[{"entity":{"id":"46e12ef9-2b67-5b52-8af9-59ce78c699f7","slug":"ahpc","display_name":"AhpC","entity_type_key":"protein"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"fad2ed93-43ff-5630-a150-69416b918bf7","slug":"catalytic-cysteine-ionization","display_name":"catalytic cysteine ionization","entity_type_key":"cellular_process"},"role":"object","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""}]},"contexts":[{"dimension":"cell_type","value_text":"Purified enzyme","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Purified Salmonella typhimurium AhpC kinetic/spectroscopic assays","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"One bacterial peroxiredoxin, not a numerical pKa for every protein.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Salmonella typhimurium","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"facd2d65-6dce-5118-92a7-4c6df1670a09","evidence_kind":"curated_literature_summary","locator":"lines 1239-1249","start_line":1239,"end_line":1249,"excerpt":"## ahpc-low-pka\n\nAn enzyme environment can make cysteine reactive near physiological pH.\n\nPurified bacterial AhpC catalytic cysteine has a measured pKa near 5.9, below the free-cysteine value generalized in the source.\n\nOrganism: Salmonella typhimurium\nCell type: Purified enzyme\nExperimental model: Purified Salmonella typhimurium AhpC kinetic/spectroscopic assays\nLimitations: One bacterial peroxiredoxin, not a numerical pKa for every protein.\nPrimary reference: [Cysteine pKa values for the bacterial peroxiredoxin AhpC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2645924/)","model_system":"Purified Salmonella typhimurium AhpC kinetic/spectroscopic 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":"2bbbd41b-bdcc-5654-8a20-bc770a55e865","title":"Free cysteine pKa does not describe every protein active site","kind":"qualification","status":"qualified","why":"AhpC catalytic cysteine is predominantly deprotonated near physiological pH, countering universal mostly asleep wording.","resolution":"Use protein-specific pKa rather than free-amino-acid values to infer catalysis.","created_at":"2026-09-17 07:19:34","record_type":"qualification","display_label":"Source qualification","record_url":"/corrections/2bbbd41b-bdcc-5654-8a20-bc770a55e865","literature_review":{"revision_id":"80984e03-5f0f-5877-8094-afef7637444e","start_line":1570,"end_line":1575,"papers":[{"paper_key":"ahpc-2009","title":"Cysteine pKa values for the bacterial peroxiredoxin AhpC","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2645924/","doi":"10.1021/bi801718d","year":2009,"model":"Purified Salmonella typhimurium AhpC kinetic/spectroscopic assays","summary":"Catalytic cysteine pKa near 5.9 counters use of free-cysteine pKa for all proteins."}]},"sides":[{"conflict_id":"2bbbd41b-bdcc-5654-8a20-bc770a55e865","ordinal":0,"label":"Original preserved statement","revision_id":"1fa1ebde-141f-5d47-8a4f-ba87ff84a6c6","start_line":51,"end_line":51,"quote":"**pKa selenol ≈ 5.2** vs **thiol ≈ 8.3.** At pH 7.4 a selenocysteine is a fully ionized **selenolate (RSe⁻)**. A cysteine is mostly protonated and asleep.","claim_id":null,"source_key":"molecular","source_title":"Selenium: the molecular cascade","claim_ids":[]},{"conflict_id":"2bbbd41b-bdcc-5654-8a20-bc770a55e865","ordinal":1,"label":"Literature correction and experimental limits","revision_id":"80984e03-5f0f-5877-8094-afef7637444e","start_line":1570,"end_line":1575,"quote":"## Free cysteine pKa does not describe every protein active site\n\nAhpC catalytic cysteine is predominantly deprotonated near physiological pH, countering universal mostly asleep wording.\n\nUse protein-specific pKa rather than free-amino-acid values to infer catalysis.\nPrimary reference: [Cysteine pKa values for the bacterial peroxiredoxin AhpC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2645924/)","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":"An enzyme environment can make cysteine reactive near physiological pH.","evidence_scope":"direct_experimental","papers":[{"key":"ahpc-2009","title":"Cysteine pKa values for the bacterial peroxiredoxin AhpC","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2645924/","doi":"10.1021/bi801718d","year":2009,"model":"Purified Salmonella typhimurium AhpC kinetic/spectroscopic assays","summary":"Catalytic cysteine pKa near 5.9 counters use of free-cysteine pKa for all proteins."}]}}