TraitMech

TraitMech › METABOLISM

Oxidative phosphorylation

METPO:1000803 · CLASS · REVIEWED

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.

Trait evidence (2)

  • DOI:10.1038/191144a0
    phosphorylation to electron and hydrogen transfer

    Mitchell's chemiosmotic proposal supports coupling electron transfer to phosphorylation.

  • DOI:10.1038/s41598-019-38564-0
    energized by the proton motive force

    Supports proton motive force-driven ATP synthesis by F1Fo ATP synthase.

Oxidative phosphorylation chemiosmotic coupling

Evidence-backed causal sketch linking respiratory electron transfer, proton motive force, ATP synthase, and ATP production.

MECHANISTIC · Represents a concrete aerobic heme-copper-oxidase branch of bacterial oxidative phosphorylation. The redundant family-unspecified terminal-oxidase node was removed rather than assigned an overbroad grounding.

Oxidative phosphorylation chemiosmotic coupling Interactive directed graph showing evidence-backed causal relationships for Oxidative phosphorylation.

Edge evidence

  • Oxidative phosphorylation uses pathway electron transport chain

    Oxidative phosphorylation couples phosphorylation to respiratory electron transfer.

    • DOI:10.1038/191144a0 electron and hydrogen transfer Mitchell paper supports coupling electron/hydrogen transfer to phosphorylation.
  • electron transport chain localized to cellular membrane biolink:located_in

    Electron transfer and proton translocation are membrane-coupled.

    • DOI:10.1038/191144a0 Chemi-Osmotic Type of Mechanism Chemiosmotic mechanism requires a membrane-separated ion gradient.
  • electron transport chain generates proton motive force biolink:produces

    Respiratory electron transfer establishes a proton motive force.

    • DOI:10.1038/s41598-019-38564-0 proton motive force (pmf) established and maintained by respiratory chain enzymes Supports respiratory chain generation of pmf.
  • proton motive force regulates F1Fo ATP synthase RO:0002211

    Proton motive force energizes F1Fo ATP synthase.

  • F1Fo ATP synthase produces ATP METPO:2007800

    ATP synthase synthesizes ATP from ADP and phosphate.

    • DOI:10.1007/BF01923429 synthesis of ATP is also driven by a proton motive force ATP synthase review supports pmf-driven ATP synthesis.
  • NADH is oxidized by Complex I / NADH:quinone oxidoreductase (NDH-1)

    Complex I oxidizes NADH at the respiratory chain entry point.

    • DOI:10.3390/ijms252413421 Proton-translocating NADH–ubiquinone oxidoreductase (complex I) catalyzes the oxidation of NADH by ubiquinone accompanied by the transmembrane transfer of four protons complex I catalyzes the oxidation of NADH by ubiquinone (general prokaryotic claim).
  • Complex I / NADH:quinone oxidoreductase (NDH-1) reduces quinone pool METPO:2007802

    Complex I transfers electrons from NADH to the quinone pool.

    • DOI:10.3390/ijms252413421 oxidation of NADH by ubiquinone oxidation of NADH by ubiquinone; reduces the membrane quinone pool.
  • Complex I / NADH:quinone oxidoreductase (NDH-1) translocates proton

    Complex I couples redox chemistry to transmembrane proton translocation.

    • DOI:10.3390/ijms252413421 accompanied by the transmembrane transfer of four protons coupled with the vectorial transmembrane transfer of four H+ ions.
  • Complex I / NADH:quinone oxidoreductase (NDH-1) generates proton motive force biolink:produces

    Complex I proton translocation contributes directly to formation of the proton motive force.

    • DOI:10.3390/ijms252413421 contributing to the formation of a proton motive force (pmf) The review directly links proton-translocating NADH-ubiquinone oxidoreductase to PMF formation across bacterial and mitochondrial coupling membranes.
  • succinate is oxidized by succinate dehydrogenase / Complex II

    Succinate dehydrogenase oxidizes succinate, reducing quinone.

    • DOI:10.1007/s10863-024-10041-y catalyzes the two-electron reduction of quinone by succinate succinate dehydrogenase catalyzes the two-electron reduction of quinone by succinate.
  • succinate dehydrogenase / Complex II reduces quinone pool METPO:2007802

    Complex II transfers electrons from succinate to the membrane quinone pool.

    • DOI:10.1007/s10863-024-10041-y catalyzes the two-electron reduction of quinone by succinate The B. licheniformis respiratory-chain study identifies succinate dehydrogenase as succinate:quinone oxidoreductase, directly joining Complex II to the quinone pool.
  • proton translocation generates proton motive force biolink:produces

    Vectorial proton translocation establishes the proton motive force.

    • DOI:10.3390/ijms252413421 contributing to the formation of a proton motive force (pmf) energy conservation in the form of an electrochemical gradient (proton motive force, pmf).
  • heme-copper oxidase reduces oxygen METPO:2007802

    Heme-copper terminal oxidases catalyze four-electron reduction of O2 to water in the concrete branch represented here.

    • DOI:10.3390/ijms25021277 catalyze the four-electron reduction of O2 to 2H2O The review identifies heme-copper oxidases as a bacterial terminal-oxidase class carrying out the oxygen-reduction reaction.
  • heme-copper oxidase translocates proton

    Heme-copper oxidases act as proton pumps contributing to PMF.

    • DOI:10.3390/ijms25021277 Heme-copper oxidases are true proton pumps Heme-copper oxidases are true proton pumps (general claim).

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
heme-copper oxidase UniProtKB:P08306
Cytochrome c oxidase subunit 2 (ctaC) 		Paracoccus denitrificans
NCBITaxon:266 		REVIEWED
retrieved 2026-08-23 · entry v167 · sequence v1

Subunit II component of purified P. denitrificans cytochrome c oxidase; this accession does not represent the complete heme-copper oxidase complex.

  • DOI:10.1016/S0005-2728(98)00092-9 enzyme containing polypeptides I-IV The primary purification study establishes the four-subunit P. denitrificans oxidase and its subunit-II component; UniProtKB P08306 verifies the reviewed protein and taxon.

Provenance

Identifier source
METPO (2026-06-12)
Author
Anthea Guo
Definition source
DOI:10.1038/191144a0

Parent traits (1)

Synonyms (1)

  • respiratory-chain phosphorylation EXACT_SYNONYM · http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo

Cross-references

  • GO:0006119

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000803 [-1.060, -0.950, -1.248, -0.351, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/metabolism/oxidative_phosphorylation-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial oxidative phosphorylation

## Trait record and scope

- **Trait label:** Oxidative phosphorylation
- **Trait identifier:** **`METPO:1000803`**
- **Category / kind / status:** METABOLISM / CLASS / REVIEWED
- **Parent:** `METPO:1000060`

### Operational definition

For TraitMech, this trait should mean the **physiological capacity to conserve energy by coupling a membrane-associated respiratory electron-transfer chain to formation of an electrochemical ion gradient, followed by ATP synthesis from ADP and inorganic phosphate through an ion-driven rotary ATP synthase**. In the canonical bacterial pathway, reducing equivalents enter through primary dehydrogenases, electrons pass through a membrane quinone pool to terminal oxidases or reductases, proton motive force (PMF) is generated, and F-type ATP synthase consumes that PMF to make ATP. Recent reviews describe the same core sequence: respiratory complexes convert NADH or FADH₂ energy into a proton electrochemical gradient, and that gradient drives ATP synthase. (tsviklist2022thecpxstress pages 1-2, zharova2023f1·foatpsynthaseatpase pages 1-2)

The trait is **not synonymous with aerobic respiration**. Oxygen is one terminal acceptor, but anaerobic respiratory chains using nitrate or other acceptors can also conserve energy through an ion gradient. Respiratory nitrate reductase Nar, for example, receives electrons from quinol and can support membrane-potential maintenance under oxygen limitation, although the demonstrated *Streptomyces coelicolor* case sustains survival rather than anaerobic growth. (sawers2019anaerobicnitraterespiration pages 1-2)

### Inclusion criteria

A positive mechanistic graph should normally contain evidence for all three modules:

1. **Respiratory redox module:** oxidation of an electron donor and reduction of a terminal acceptor through a membrane-associated chain.
2. **Chemiosmotic module:** generation or maintenance of an H⁺ or, in a defined microbial variant, Na⁺ electrochemical gradient across an energy-transducing membrane.
3. **ATP-synthesis module:** gradient-driven ATP formation by F-type or archaeal/prokaryotic A/V-type ATP synthase.

### Boundary cases

- **Substrate-level phosphorylation** is outside scope because ATP is formed by direct phosphoryl transfer rather than through a respiratory ion gradient.
- **Fermentation alone** is outside scope. Fermentative metabolism may supply respiratory donors, but fermentation does not establish this trait unless an ion-motive respiratory chain and ATP synthase are also demonstrated.
- **Photophosphorylation** is a neighboring but distinct trait: photosystem II and cytochrome b₆f use light-driven electron transfer to generate the gradient. The respiratory bc₁/bcc complexes belong here; photosynthetic b₆f should not be imported into this graph merely because it uses a homologous Q-cycle. (kao2022quinonebindingsites pages 1-3)
- **Flavin-based electron bifurcation alone** is not oxidative phosphorylation. It directly couples exergonic and endergonic redox reactions in a soluble complex and “is not coupled to ATP synthesis”; it can nevertheless be an upstream donor-generating module when reduced ferredoxin subsequently feeds an ion-motive respiratory chain. (muller2018electronbifurcationa pages 1-2)
- **ATP hydrolysis-driven maintenance of PMF** is the reverse activity of an ATPase, not evidence of oxidative phosphorylation unless net gradient-driven ATP synthesis is shown. Some bacterial and archaeal enzymes are physiologically unidirectional or strongly regulated. (zharova2023f1·foatpsynthaseatpase pages 1-2)
- **Presence of respiratory genes alone** establishes genomic potential, not an observed phenotype. This is especially important for MAG-derived reconstructions.

## Candidate nodes

Identifiers below are conservative. Where exact cross-ontology grounding is uncertain or taxon-dependent, a label-only node is preferable to an invented or overly broad CURIE.

### Trait, pathways, and processes

| Candidate node | Suggested grounding | Curation note |
|---|---|---|
| Oxidative phosphorylation | `METPO:1000803` | Root trait node; quote identifier verbatim. |
| Respiratory electron-transport chain | GO term to be selected after ontology lookup; otherwise label-only | Should encompass primary dehydrogenase → quinone → terminal reductase/oxidase. |
| Chemiosmotic coupling | Label-only, or reviewed GO term | Mechanistic bridge between redox chemistry and ATP synthesis. |
| Proton motive force | Label-only; do not equate automatically with a proton-transport GO process | PMF contains electrical and chemical components. |
| Sodium motive force | Label-only | Valid alternative in particular bacteria and archaea, not universal. |
| ATP synthesis coupled to ion translocation | EC/GO term after validation | Product-level endpoint of the graph. |
| Aerobic respiration | GO-groundable neighboring process | A subtype/context, not equivalent to the target trait. |
| Anaerobic respiration | GO-groundable neighboring process | Include only when an alternative acceptor supports ion-gradient energy conservation. |

### Complexes, enzymes, genes, and proteins

| Candidate node | Suggested grounding | Representative genes or subunits | Notes |
|---|---|---|---|
| Proton-translocating NADH:quinone oxidoreductase, complex I/NDH-1 | `EC:7.1.1.2` | bacterial `nuoA–N`; mycobacterial `nuoABCDEFGHIJKLMN` | Oxidizes NADH, reduces quinone, translocates four H⁺ per NADH/2 e⁻ in the canonical enzyme. (grivennikova2024protontranslocatingnadh–ubiquinoneoxidoreductase pages 1-2, bajeli2020terminalrespiratoryoxidases pages 1-2) |
| Type II NADH dehydrogenase, NDH-2 | Label-only pending exact EC confirmation | `ndh`, `ndhA` in *M. tuberculosis* | Feeds electrons to quinone but is non-proton-pumping in the cited mycobacterial system. (bajeli2020terminalrespiratoryoxidases pages 1-2) |
| Succinate dehydrogenase, complex II | `EC:1.3.5.1` | `sdhABCD` family | Connects the TCA cycle to the quinone pool; generally not a primary PMF generator. (borisov2023cytochromebdas pages 1-3, tsviklist2022thecpxstress pages 1-2) |
| Na⁺-translocating NADH:quinone oxidoreductase | Label-only; validate EC/KEGG module before import | `nqrA–F` | Variant primary sodium pump; should be a conditional branch. (mulkidjanian2008thepastand pages 1-2) |
| Cytochrome bc₁ complex | Label-only complex node | `petABC`/taxon-specific nomenclature | Quinol oxidation and Q-cycle proton translocation. |
| Cytochrome bcc–aa₃ supercomplex | Label-only complex node | `qcrABC`, `cta` genes, taxon-specific | Important actinobacterial/mycobacterial branch. |
| Heme-copper terminal oxidase | Label-only superclass | `cyoABCD`, `cox/cta` families | Reduces O₂; pumping stoichiometry varies by family. |

Showing the first 60 of 285 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Paracoccus denitrificans NCBITaxon:266 PMID:30428155 Free-living model of the mitochondrial-type respiratory chain and oxidative phosphorylation (full set of bacterial respiratory complexes).

Curation history

  1. · CURATE_PROTEIN_TAXON_EXAMPLE · codex

    Reviewed the graph as mechanistic, grounded complexes I, II, and ATP synthase, replaced the ambiguous terminal-oxidase node with the cited heme-copper branch, connected the respiratory entry branches, and added DOI-backed P. denitrificans subunit-II P08306.

  2. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  3. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for chemiosmotic coupling, proton motive force, ATP synthase, and ATP production.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in×1, biolink:produces×1).

  6. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1.

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1).

  9. · RETYPE_CAUSAL_NODES · claude

    Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.

  10. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.

  11. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017×2, biolink:produces×1).

  12. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:24636×1).

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2U9ILE5×1).

  14. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces, 2 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.

  15. · NORMALISE_NODE_TYPE · claude

    Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.

  16. · NORMALISE_NODE_SENSE · claude

    One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition — the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).

  17. · REVIEW_UNIPROT_INSTANCE_GROUNDINGS · codex

    Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).

  18. · RESTORE_CANONICAL_CITATION · claude

    Restored the canonical-example citation for NCBITaxon:266 from DOI:10.1016/S0005-2728(98)00092-9 back to PMID:30428155 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.

  19. · ADD_EXACT_ONTOLOGY_MATCH · codex

    Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0006119; declared exact synonym(s): 'respiratory-chain phosphorylation'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.