Summary: Cytochrome oxidase c subunit VIb
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This is the Wikipedia entry entitled "Cytochrome c oxidase". More...
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Cytochrome c oxidase Edit Wikipedia article
The enzyme cytochrome c oxidase is a large transmembrane protein found in the mitochondrion and is the terminal electron acceptor in the electron transfer chain, taking four reducing equivalents from cytochrome c and converting molecular oxygen to water. In the process, it translocates protons, helping to establish a chemiosmotic potential that ATP synthase then uses to synthesize ATP.
4 Fe+2-cyochrome c + 4H+ + O2 â†’ 4 Fe+3-cytochrome c + H20.
The complex is a large lipoprotein comprised of a number of metal prosthetic sites and 13 protein subunits, which in mammals, 10 are nuclear in origin and 3 are synthesized mitochondrially. The complex contains 2 cytochromes, the a and a3 cytochromes, and two copper centers, the CuA and CuB centers. In fact, the cytochrome a3 and CuB are a binuclear center and this is the site of oxygen reduction. The mechanism of action of this large complex is still an active research topic.
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Cytochrome oxidase c subunit VIb Provide feedback
Cytochrome c oxidase, a 13 sub-unit complex, EC:126.96.36.199 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.
Carrero-Valenzuela RD, Quan F, Lightowlers R, Kennaway NG, Litt M, Forte M; , Gene 1991;102:229-236.: Human cytochrome c oxidase subunit VIb: characterization and mapping of a multigene family. PUBMED:1651883 EPMC:1651883
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003213
Cytochrome c oxidase ( EC ) is an oligomeric enzymatic complex that is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen [ PUBMED:6307356 ]. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane.
In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptide subunits. One of these subunits is the potentially haem-binding subunit, VIb, which is encoded in the nucleus [ PUBMED:11136449 ]. Subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex [ PUBMED:12874793 , PUBMED:16364442 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||respiratory chain complex IV (GO:0045277)|
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This family is a member of clan CHCH (CL0351), which has the following description:
The conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain) superfamily members include NADH-ubiquinone oxidoreductases, some cytochrome oxidases and yeast mitochondrial ribosomal proteins. Within each helix of the CHCH domain there are two cysteines present in a C-X9-C motif.
The clan contains the following 8 members:CHCH Cmc1 COX17 COX6B CX9C MTCP1 NDUF_B7 Ndufs5
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. 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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Curation and family details
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|Seed source:||Pfam-B_9188 (release 5.2)|
|Author:||Mian N , Bateman A|
|Number in seed:||57|
|Number in full:||3590|
|Average length of the domain:||66.6 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||54.45 %|
|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:||20|
|Download:||download the raw HMM for this family|
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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:
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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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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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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 COX6B domain has been found. There are 136 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.