cytochrome bd-I ubiquinol oxidase complex

cellstructuremech:cytochrome_bd_i_ubiquinol_oxidase_complex · Energy complex · Multiprotein complex · Proposed

Cytochrome bd-I ubiquinol oxidase complex is a membrane-bound CydAB respiratory terminal oxidase with small bd-I accessory subunits that oxidizes ubiquinol, reduces molecular oxygen to water, and contributes to the respiratory proton motive force. [DOI:10.1126/science.aay0967]

Synonyms: cytochrome bd-I oxidase

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
cytochrome bd-I ubiquinol oxidase subunit I	Protein	part of	`InterPro:IPR002585`	cydA	ESSENTIAL	Large membrane subunit of the cytochrome bd-I terminal oxidase core that houses heme cofactors used for ubiquinol-to-oxygen electron flow. `InterPro:IPR002585` InterPro IPR002585 is the cytochrome ubiquinol oxidase subunit-1 family and includes the E. coli CydA example. `PDB:6RKO` RCSB maps PDB:6RKO polymer entity 2 to E. coli K-12 cytochrome bd-I ubiquinol oxidase subunit 1, UniProtKB:P0ABJ9.
cytochrome bd-I ubiquinol oxidase subunit II	Protein	part of	`InterPro:IPR003317`	cydB	ESSENTIAL	Second large membrane subunit of the CydAB cytochrome bd-I oxidase core. `InterPro:IPR003317` InterPro IPR003317 is the cytochrome ubiquinol oxidase subunit-2 family and includes the E. coli CydB example. `PDB:6RKO` RCSB maps PDB:6RKO polymer entity 1 to E. coli K-12 cytochrome bd-I ubiquinol oxidase subunit 2, UniProtKB:P0ABK2.
cytochrome bd-I ubiquinol oxidase CydX small subunit	Protein	part of	`InterPro:IPR011724`	cydX, ybgT	UNKNOWN	Small single-pass membrane subunit resolved in the E. coli bd-I oxidase. `InterPro:IPR011724` InterPro IPR011724 is the Cyd operon protein YbgT family, including the E. coli CydX/YbgT subunit. `PDB:6RKO` RCSB maps PDB:6RKO polymer entity 4 to E. coli K-12 cytochrome bd-I ubiquinol oxidase subunit X, UniProtKB:P56100.
YnhF-like cytochrome bd-I small subunit	Protein	part of	`InterPro:IPR047743`	ynhF	UNKNOWN	YnhF-like single-pass membrane subunit resolved with the E. coli bd-I oxidase and associated with a CydH NCBIfam model. `InterPro:IPR047743` InterPro IPR047743 is the YnhF-like membrane-protein family and includes an NCBIfam model for cytochrome bd-I oxidase CydH. `PDB:6RKO` RCSB maps PDB:6RKO polymer entity 3 to E. coli K-12 YnhF, UniProtKB:A5A618.

Canonical examples

NCBITaxon:562 Escherichia coli — Bacterial species used for the four-subunit cytochrome bd-I oxidase structure deposited as PDB:6RKO. [PDB:6RKO]

Functions

ubiquinol:oxygen terminal oxidase activity — Cytochrome bd-I oxidizes ubiquinol, reduces molecular oxygen to water, and conserves respiratory-chain energy through a bd-type architecture distinct from heme-copper cytochrome c oxidases.
- InterPro:IPR002585 InterPro describes CydA-family proteins as alternative oxidases that oxidize ubiquinol and reduce oxygen as part of the electron transport chain.
- DOI:10.1126/science.aay0967 Safarian et al. 2019 solved the E. coli cytochrome bd-I oxidase structure deposited as PDB:6RKO.
- PMID:31604309 The PubMed abstract for Safarian et al. 2019 describes cytochrome bd-type quinol oxidases as respiratory-chain enzymes that catalyze molecular-oxygen reduction to water and are structurally unrelated to mitochondrial cytochrome c oxidases.

Mechanism graphs

Cytochrome bd-I reduces oxygen with ubiquinol electrons (FUNCTION)

Cytochrome bd-I oxidase converts ubiquinol and oxygen to ubiquinone and water through its CydA and CydB large subunits and contributes to respiratory energy conservation.

Subject	Predicate	Object	Evidence
cytochrome bd-I ubiquinol oxidase complex	enables	ubiquinol:oxygen terminal oxidase activity	`PDB:6RKO` PDB:6RKO resolves the four-subunit E. coli cytochrome bd-I oxidase structure.
cytochrome bd-I ubiquinol oxidase subunit I	contributes to	ubiquinol:oxygen terminal oxidase activity	`PDB:6RKO` PDB:6RKO resolves E. coli CydA in the four-subunit cytochrome bd-I oxidase structure.
cytochrome bd-I ubiquinol oxidase subunit II	contributes to	ubiquinol:oxygen terminal oxidase activity	`PDB:6RKO` PDB:6RKO resolves E. coli CydB in the four-subunit cytochrome bd-I oxidase structure.
ubiquinol	donates electrons to	ubiquinol:oxygen terminal oxidase activity	`InterPro:IPR002585` InterPro IPR002585 describes CydA-family oxidases as oxidizing ubiquinol as part of an electron transport chain.
molecular oxygen	accepts electrons in	ubiquinol:oxygen terminal oxidase activity	`InterPro:IPR002585` InterPro IPR002585 describes the family as reducing oxygen while oxidizing ubiquinol.
ubiquinol:oxygen terminal oxidase activity	produces	ubiquinone	`InterPro:IPR002585` InterPro IPR002585 describes CydA-family oxidases as oxidizing ubiquinol as part of an electron transport chain.
ubiquinol:oxygen terminal oxidase activity	produces	water	`PMID:31604309` The PubMed abstract for Safarian et al. 2019 states that bd-type quinol oxidases catalyze molecular-oxygen reduction to water.
ubiquinol:oxygen terminal oxidase activity	contributes to	transmembrane proton motive force	`PDB:6RKO` RCSB annotates the PDB:6RKO CydA, CydB, and CydX entities with EC 7.1.1.7, quinol oxidase (electrogenic, proton-motive force generating).

Discussions

CURATION_TODO (OPEN): Resolve how CydX/YbgT and YnhF-like small subunits should be split across cytochrome bd-I, bd-II, and two-subunit CydAB oxidases. PDB:6RKO supports a four-subunit E. coli bd-I oxidase with CydX and YnhF, while PDB:7NKZ supports a two-subunit Mycobacterium tuberculosis bd oxidase; this record should not project E. coli bd-I small subunits onto every bd-type oxidase.

Evidence

GO:0098803 Gene Ontology cellular-component term for respiratory-chain protein complexes.
GO:0070069 Gene Ontology cellular-component term for cytochrome complexes.
GO:0016682 Gene Ontology molecular-function term for oxidoreductase activity with a diphenol-related donor and oxygen as acceptor; no exact cytochrome bd ubiquinol oxidase activity term was found.
InterPro:IPR002585 InterPro family for cytochrome ubiquinol oxidase subunit 1.
InterPro:IPR003317 InterPro family for cytochrome ubiquinol oxidase subunit 2.
InterPro:IPR011724 InterPro family for the CydX/YbgT small subunit.
InterPro:IPR047743 InterPro family for the YnhF-like CydH small subunit.
DOI:10.1126/science.aay0967 Safarian et al. 2019, Active site rearrangement and structural divergence in prokaryotic respiratory oxidases, Science.
PMID:31604309 PubMed identifier for Safarian et al. 2019 as reported by the RCSB PDB:6RKO primary citation.
PDB:6RKO RCSB Protein Data Bank entry for the E. coli cytochrome bd-I oxidase structure from Safarian et al. 2019.

Curation history

2026-09-24T06:59:35Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-24T07:00:39Z codex · EXPANDED_RECORD — Added respiratory-chain and cytochrome-complex parentage, PDB:6RKO E. coli cytochrome bd-I oxidase components with InterPro CydA, CydB, CydX, and YnhF-like family groundings, UniProtKB-backed gene aliases, terminal ubiquinol:oxygen oxidase function, literature/PDB evidence, a compact bd-I function graph, and a small-subunit scope TODO.
2026-09-24T07:02:54Z codex · REFINED_GRAPH — Replaced the orphan CydAB graph node with direct CydA and CydB contribution edges and grounded water production in PMID:31604309.
2026-09-24T07:13:46Z codex · ADDRESSED_REVIEW — Addressed review issues #1462, #1463, and #1464 by adding a ubiquinone product node and edge, narrowing the YnhF/CydH role wording, and tying the heme-copper divergence claim to PMID:31604309.

Source: data/structures/energy_complex/cytochrome_bd_i_ubiquinol_oxidase_complex.yaml