{"id":"25ebc281-967b-53d2-844f-84724cc22e12","stable_key":"649e861b-265a-5912-bc36-3a73e53ef892:l-serine-pss1-calcium","predicate":"organizes_active_site_of","statement":"Human PSS1 structures positioned calcium and serine in the catalytic pocket; structural and mutational analysis implicated His172 in the base-exchange mechanism.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"24afe76f-0d1f-59b6-84f9-e7687873b7c9","mechanism_event_label":"Calcium has a constructive catalytic role in this lipid-building enzyme.","subject":{"id":"e359bc15-e675-5d83-b0fe-1d70814e130b","slug":"calcium-ion","display_name":"Calcium ion","entity_type_key":"ion"},"object":{"id":"0b5548b5-3cd8-5f19-8eea-dfae2a671fb3","slug":"ptdss1","display_name":"Human phosphatidylserine synthase 1 / PTDSS1","entity_type_key":"protein"},"evidence_count":1,"mechanism_event":{"id":"24afe76f-0d1f-59b6-84f9-e7687873b7c9","stable_key":"649e861b-265a-5912-bc36-3a73e53ef892:l-serine-pss1-calcium-event","event_type":"observed_relationship","label":"Calcium has a constructive catalytic role in this lipid-building enzyme.","description":"Human PSS1 structures positioned calcium and serine in the catalytic pocket; structural and mutational analysis implicated His172 in the base-exchange mechanism.","status":"provisional","compartment":null,"participants":[{"entity":{"id":"e359bc15-e675-5d83-b0fe-1d70814e130b","slug":"calcium-ion","display_name":"Calcium ion","entity_type_key":"ion"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"0b5548b5-3cd8-5f19-8eea-dfae2a671fb3","slug":"ptdss1","display_name":"Human phosphatidylserine synthase 1 / PTDSS1","entity_type_key":"protein"},"role":"target","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"c882cd0b-9d83-5b07-bd1c-fe4d45657dcb","slug":"l-serine","display_name":"L-Serine","entity_type_key":"small_molecule"},"role":"context_participant","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""}]},"contexts":[{"dimension":"evidence_access","value_text":"Primary full text","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Full-length human PSS1 cryo-EM in apo, calcium-bound and calcium/serine-bound states.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"The proposed chemical mechanism combines structure and mutagenesis; it is not a clinical calcium-response experiment.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"L-Serine collection; species, compartment, exposure, co-substrates and manipulation remain explicit.","comparator":null,"unit":null,"notes":"","entity":{"slug":"l-serine","display_name":"L-Serine","entity_type_key":"small_molecule"}},{"dimension":"plain_language","value_text":"Calcium has a constructive catalytic role in this lipid-building enzyme.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"Structural basis for catalytic mechanism of human phosphatidylserine synthase 1. · 2025 · https://pubmed.ncbi.nlm.nih.gov/40044636/ · DOI 10.1038/s41421-025-00775-3","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"535240b4-0271-559c-b35c-8525930dae73","evidence_kind":"source_excerpt","locator":"Lines 254-260","start_line":254,"end_line":260,"excerpt":"## l-serine-pss1-calcium\nCalcium has a constructive catalytic role in this lipid-building enzyme.\nHuman PSS1 structures positioned calcium and serine in the catalytic pocket; structural and mutational analysis implicated His172 in the base-exchange mechanism.\nModel: Full-length human PSS1 cryo-EM in apo, calcium-bound and calcium/serine-bound states.\nLimitations: The proposed chemical mechanism combines structure and mutagenesis; it is not a clinical calcium-response experiment.\nEvidence access: Primary full text\nStructural basis for catalytic mechanism of human phosphatidylserine synthase 1. · 2025 · https://pubmed.ncbi.nlm.nih.gov/40044636/ · DOI 10.1038/s41421-025-00775-3","model_system":"Full-length human PSS1 cryo-EM in apo, calcium-bound and calcium/serine-bound states.","directness":"reported_statement","verification_status":"source_derived_draft","notes":"Original curation paraphrase; evidence access and experimental limitations specified.","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"70bcf57a-36bb-563f-9073-2d616e5f155a","stable_key":"import-649e861b-265a-5912-bc36-3a73e53ef892","title":"L-Serine: synthesis, one-carbon metabolism, lipids and cross-nutrient mechanisms (2026-09-19)","document_type":"imported_text","citation_label":"AI-assisted research curation; primary references, access levels and experimental limitations individually identified. 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