identifier: METPO:1000803 label: Oxidative phosphorylation definition: A metabolism that generates ATP through the transfer of electrons from electron donors to electron acceptors via redox reactions, coupled to the pumping of protons across a membrane to create an electrochemical gradient. definition_source: DOI:10.1038/191144a0 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000060 created_by: Anthea Guo evidence: - reference: DOI:10.1038/191144a0 snippet: phosphorylation to electron and hydrogen transfer notes: Mitchell's chemiosmotic proposal supports coupling electron transfer to phosphorylation. - reference: DOI:10.1038/s41598-019-38564-0 snippet: energized by the proton motive force notes: Supports proton motive force-driven ATP synthesis by F1Fo ATP synthase. canonical_examples: - taxon_id: NCBITaxon:266 taxon_label: Paracoccus denitrificans note: "Free-living model of the mitochondrial-type respiratory chain and oxidative phosphorylation (full set of bacterial respiratory complexes)." reference: PMID:30428155 causal_graphs: - graph_id: oxidative_phosphorylation_chemiosmotic_coupling title: Oxidative phosphorylation chemiosmotic coupling description: Evidence-backed causal sketch linking respiratory electron transfer, proton motive force, ATP synthase, and ATP production. nodes: - node_id: oxidative_phosphorylation_trait label: Oxidative phosphorylation node_type: TRAIT grounding: METPO:1000803 description: ATP generation coupled to redox-driven ion gradients. - node_id: electron_transport_chain label: electron transport chain node_type: PATHWAY grounding: GO:0022900 description: Membrane-associated electron transfer pathway. - node_id: cellular_membrane label: cellular membrane node_type: CELLULAR_LOCALIZATION grounding: GO:0016020 description: Membrane across which ions are translocated. - node_id: proton_motive_force label: proton motive force node_type: STATE description: Transmembrane electrochemical proton gradient. grounding: METPO:1007500 - node_id: atp_synthase label: F1Fo ATP synthase node_type: GENE_OR_PROTEIN description: Rotary enzyme complex that synthesizes ATP using ion motive force. - node_id: atp label: ATP node_type: CHEMICAL grounding: CHEBI:30616 description: Energy-rich nucleotide product. - node_id: nadh label: NADH node_type: CHEMICAL description: Reduced electron donor feeding the respiratory chain. - node_id: complex_i label: Complex I / NADH:quinone oxidoreductase (NDH-1) node_type: GENE_OR_PROTEIN description: Proton-translocating NADH:quinone oxidoreductase entry complex. - node_id: succinate label: succinate node_type: CHEMICAL description: Electron donor oxidized by succinate dehydrogenase. - node_id: succinate_dehydrogenase label: succinate dehydrogenase / Complex II node_type: GENE_OR_PROTEIN description: Complex II coupling succinate oxidation to quinone reduction. - node_id: quinone_pool label: quinone pool node_type: CHEMICAL description: Membrane quinone/quinol electron carrier pool (ubiquinone/menaquinone). - node_id: proton label: proton node_type: CHEMICAL description: Translocated ion forming the transmembrane gradient. grounding: CHEBI:24636 - node_id: proton_translocation label: proton translocation node_type: BIOLOGICAL_PROCESS description: Vectorial transmembrane transfer of protons by respiratory complexes. - node_id: terminal_oxidase label: terminal oxidase node_type: GENE_OR_PROTEIN description: Respiratory enzyme reducing molecular oxygen to water. grounding: UniProtKB:A0A2U9ILE5 - node_id: oxygen label: oxygen node_type: CHEMICAL description: Terminal electron acceptor in aerobic respiration. - node_id: heme_copper_oxidase label: heme-copper oxidase node_type: GENE_OR_PROTEIN description: Proton-pumping terminal oxidase class. edges: - subject: oxidative_phosphorylation_trait predicate: uses pathway object: electron_transport_chain description: Oxidative phosphorylation couples phosphorylation to respiratory electron transfer. evidence: - reference: DOI:10.1038/191144a0 snippet: electron and hydrogen transfer notes: Mitchell paper supports coupling electron/hydrogen transfer to phosphorylation. - subject: electron_transport_chain predicate: localized to object: cellular_membrane description: Electron transfer and proton translocation are membrane-coupled. evidence: - reference: DOI:10.1038/191144a0 snippet: Chemi-Osmotic Type of Mechanism notes: Chemiosmotic mechanism requires a membrane-separated ion gradient. predicate_id: biolink:located_in - subject: electron_transport_chain predicate: generates object: proton_motive_force description: Respiratory electron transfer establishes a proton motive force. evidence: - reference: DOI:10.1038/s41598-019-38564-0 snippet: proton motive force (pmf) established and maintained by respiratory chain enzymes notes: Supports respiratory chain generation of pmf. predicate_id: biolink:produces - subject: proton_motive_force predicate: regulates object: atp_synthase description: Proton motive force energizes F1Fo ATP synthase. evidence: - reference: DOI:10.1038/s41598-019-38564-0 snippet: energized by the proton motive force notes: Supports pmf-driven ATP synthase. predicate_id: RO:0002211 - subject: atp_synthase predicate: produces object: atp description: ATP synthase synthesizes ATP from ADP and phosphate. evidence: - reference: DOI:10.1007/BF01923429 snippet: synthesis of ATP is also driven by a proton motive force notes: ATP synthase review supports pmf-driven ATP synthesis. predicate_id: METPO:2000202 - subject: nadh predicate: is oxidized by object: complex_i description: Complex I oxidizes NADH at the respiratory chain entry point. evidence: - reference: DOI:10.3390/ijms252413421 notes: complex I catalyzes the oxidation of NADH by ubiquinone (general prokaryotic claim). - subject: complex_i predicate: reduces object: quinone_pool description: Complex I transfers electrons from NADH to the quinone pool. evidence: - reference: DOI:10.3390/ijms252413421 notes: oxidation of NADH by ubiquinone; reduces the membrane quinone pool. predicate_id: METPO:2000017 - subject: complex_i predicate: translocates object: proton description: Complex I couples redox chemistry to transmembrane proton translocation. evidence: - reference: DOI:10.3390/ijms252413421 notes: coupled with the vectorial transmembrane transfer of four H+ ions. - subject: succinate predicate: is oxidized by object: succinate_dehydrogenase description: Succinate dehydrogenase oxidizes succinate, reducing quinone. evidence: - reference: DOI:10.1007/s10863-024-10041-y notes: succinate dehydrogenase catalyzes the two-electron reduction of quinone by succinate. - subject: proton_translocation predicate: generates object: proton_motive_force description: Vectorial proton translocation establishes the proton motive force. evidence: - reference: DOI:10.3390/ijms252413421 notes: energy conservation in the form of an electrochemical gradient (proton motive force, pmf). predicate_id: biolink:produces - subject: terminal_oxidase predicate: reduces object: oxygen description: Terminal oxidases catalyze four-electron reduction of O2 to water. evidence: - reference: DOI:10.3390/ijms25021277 notes: Terminal oxidases catalyze four-electron reduction of O2 to 2H2O (general bacterial claim). predicate_id: METPO:2000017 - subject: heme_copper_oxidase predicate: translocates object: proton description: Heme-copper oxidases act as proton pumps contributing to PMF. evidence: - reference: DOI:10.3390/ijms25021277 notes: Heme-copper oxidases are true proton pumps (general claim). curation_history: - timestamp: '2026-05-05T01:35:46.912667+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-07T00:00:00-07:00' curator: codex action: ADDED_CAUSAL_GRAPH changes: Added DOI-backed causal graph for chemiosmotic coupling, proton motive force, ATP synthase, and ATP production. llm_assisted: true - timestamp: '2026-05-20T03:35:30Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1). llm_assisted: true - timestamp: '2026-05-23T08:21:49Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in×1, biolink:produces×1). llm_assisted: true - timestamp: '2026-05-24T04:13:19Z' curator: claude action: RENAME_PREDICATE_LABELS changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1.' llm_assisted: true - timestamp: '2026-05-24T04:13:21Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1). llm_assisted: true - timestamp: '2026-05-24T04:41:04Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1). llm_assisted: true - timestamp: '2026-05-26T02:30:13Z' curator: claude action: RETYPE_CAUSAL_NODES changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.' llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:12Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017×2, biolink:produces×1). llm_assisted: true - timestamp: '2026-06-24T17:21:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:24636×1). llm_assisted: true - timestamp: '2026-06-26T07:15:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2U9ILE5×1). llm_assisted: true