Summary: Cytochrome bd terminal oxidase subunit II
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This is the Wikipedia entry entitled "Ubiquinol oxidase (H%2B-transporting)". More...
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Ubiquinol oxidase (H%2B-transporting) Edit Wikipedia article
|Ubiquinol oxidase (H+-transporting)|
|PDB structures||RCSB PDB PDBe PDBsum|
Ubiquinol oxidase (H+-transporting) (EC 18.104.22.168, cytochrome bb3 oxidase, cytochrome bo oxidase, cytochrome bd-I oxidase) is an enzyme with systematic name ubiquinol:O2 oxidoreductase (H+-transporting). This enzyme catalyses the following chemical reaction
- Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, WikstrÃ¶m M (October 2000). "The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site". Nature Structural Biology. 7 (10): 910â€“7. doi:10.1038/82824. PMIDÂ 11017202. S2CIDÂ 6300175.
- 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): 3657â€“62. Bibcode:2005PNAS..102.3657B. doi:10.1073/pnas.0405683102. PMCÂ 553295. PMIDÂ 15728392.
- 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): 1924â€“32. doi:10.1016/j.bbabio.2010.04.011. PMCÂ 2922442. PMIDÂ 20416270.
- 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): 18464â€“72. doi:10.1074/jbc.M110.118448. PMCÂ 2881772. PMIDÂ 20392690.
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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 . 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 . The family forms an integral functional unit with subunit I, family Bac_Ubq_Cox, PF01654.
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
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 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Seed source:||Pfam-B_997 (release 5.2)|
|Previous IDs:||Cyto_ox_2; Cyt_bd_oxidas_I;|
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
|Protein||Predicted structure||External Information|
|O06139||View 3D Structure||Click here|
|O34505||View 3D Structure||Click here|
|P0ABK2||View 3D Structure||Click here|
|P0ABK4||View 3D Structure||Click here|
|P26458||View 3D Structure||Click here|
|P45020||View 3D Structure||Click here|
|P94365||View 3D Structure||Click here|
|Q2FZH2||View 3D Structure||Click here|