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5  structures 4713  species 0  interactions 7112  sequences 8  architectures

Family: Cyt_bd_oxida_II (PF02322)

Summary: Cytochrome bd terminal oxidase subunit II

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This is the Wikipedia entry entitled "Ubiquinol oxidase (H%2B-transporting)". More...

Ubiquinol oxidase (H%2B-transporting) Edit Wikipedia article

Ubiquinol oxidase (H+-transporting)
EC no.
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PDB structuresRCSB PDB PDBe PDBsum

Ubiquinol oxidase (H+-transporting) (EC, cytochrome bb3 oxidase, cytochrome bo oxidase, cytochrome bd-I oxidase) is an enzyme with systematic name ubiquinol:O2 oxidoreductase (H+-transporting).[1][2][3][4] This enzyme catalyses the following chemical reaction

2 ubiquinol + O2 + n H+in 2 ubiquinone + 2 H2O + n H+out

Ubiquinol oxidase contains a dinuclear centre comprising two hemes, or heme and copper.


  1. ^ Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, Wikström M (October 2000). "The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site". Nature Structural Biology. 7 (10): 910–7. doi:10.1038/82824. PMID 11017202. S2CID 6300175.
  2. ^ Belevich I, Borisov VB, Zhang J, Yang K, Konstantinov AA, Gennis RB, Verkhovsky MI (March 2005). "Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site". Proceedings of the National Academy of Sciences of the United States of America. 102 (10): 3657–62. Bibcode:2005PNAS..102.3657B. doi:10.1073/pnas.0405683102. PMC 553295. PMID 15728392.
  3. ^ Yap LL, Lin MT, Ouyang H, Samoilova RI, Dikanov SA, Gennis RB (December 2010). "The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1797 (12): 1924–32. doi:10.1016/j.bbabio.2010.04.011. PMC 2922442. PMID 20416270.
  4. ^ Shepherd M, Sanguinetti G, Cook GM, Poole RK (June 2010). "Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism". The Journal of Biological Chemistry. 285 (24): 18464–72. doi:10.1074/jbc.M110.118448. PMC 2881772. PMID 20392690.

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome bd terminal oxidase subunit II Provide feedback

This family consists of cytochrome bd type terminal oxidases that catalyse quinol-dependent, Na+-independent oxygen uptake [2]. Members of this family are integral membrane proteins and contain a protohaem IX centre B558. One member of the family O05192 is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae [1]. The family forms an integral functional unit with subunit I, family Bac_Ubq_Cox, PF01654.

Literature references

  1. Juty NS, Moshiri F, Merrick M, Anthony C, Hill S; , Microbiology 1997;143:2673-2683.: The Klebsiella pneumoniae cytochrome bd' terminal oxidase complex and its role in microaerobic nitrogen fixation. PUBMED:9274021 EPMC:9274021

  2. Sturr MG, Krulwich TA, Hicks DB; , J Bacteriol 1996;178:1742-1749.: Purification of a cytochrome bd terminal oxidase encoded by the Escherichia coli app locus from a delta cyo delta cyd strain complemented by genes from Bacillus firmus OF4. PUBMED:8626304 EPMC:8626304

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003317

These proteins are cytochrome bd type terminal oxidases that catalyse quinol dependent, Na + independent oxygen uptake [ PUBMED:8626304 ]. Members of this family are integral membrane proteins and contain a protoheame IX centre B558.

Cytochrome bd may play an important role in microaerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae, where it is expressed under all conditions that permit diazotrophy [ PUBMED:9274021 ].

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Domain organisation

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Seed source: Pfam-B_997 (release 5.2)
Previous IDs: Cyto_ox_2; Cyt_bd_oxidas_I;
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 581
Number in full: 7112
Average length of the domain: 321.80 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 94.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 35.6 35.6
Trusted cut-off 36.2 36.0
Noise cut-off 35.4 35.3
Model length: 303
Family (HMM) version: 18
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Cyt_bd_oxida_II domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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