Summary: Cytochrome b(C-terminal)/b6/petD
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Cytochrome b Edit Wikipedia article
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Mitochondrial cytochrome bc1 complex
|SCOPe||3bcc / SUPFAM|
Cytochrome b is a protein found in the mitochondria of eukaryotic cells. It functions as part of the electron transport chain and is the main subunit of transmembrane cytochrome bc1 and b6f complexes.
In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (EC 126.96.36.199) â€” also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is an analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (EC 188.8.131.52), also known as the b6f complex. These complexes are involved in electron transport, the pumping of protons to create a proton-motive force (PMF). This proton gradient is used for the generation of ATP. These complexes play a vital role in cells.
Cytochrome b/b6 is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. Cytochrome b/b6 non-covalently binds two heme groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two heme groups.
Use in phylogenetics
Cytochrome b is commonly used as a region of mitochondrial DNA for determining phylogenetic relationships between organisms, due to its sequence variability. It is considered to be most useful in determining relationships within families and genera. Comparative studies involving cytochrome b have resulted in new classification schemes and have been used to assign newly described species to a genus as well as to deepen the understanding of evolutionary relationships.
Human genes encoding cytochrome b proteins include:
- CYB5A â€“ cytochrome b5 type A (microsomal)
- CYB5B â€“ cytochrome b5 type B (outer mitochondrial membrane)
- CYBASC3 â€“ cytochrome b, ascorbate dependent 3
- MT-CYB â€“ mitochondrially encoded cytochrome b
- Howell N (August 1989). "Evolutionary conservation of protein regions in the proton motive cytochrome b and their possible roles in redox catalysis". J. Mol. Evol. 29 (2): 157â€“69. doi:10.1007/BF02100114. PMID 2509716.
- Esposti MD, De Vries S, Crimi M, Ghelli A, Patarnello T, Meyer A (July 1993). "Mitochondrial cytochrome b: evolution and structure of the protein" (PDF). Biochim. Biophys. Acta. 1143 (3): 243â€“71. doi:10.1016/0005-2728(93)90197-N. PMID 8329437.
- Blankenship, Robert (2009). Molecular Mechanisms of Photosynthesis. Blackwell Publishing. pp. 124â€“132.
- Howell N (1989). "Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis". J. Mol. Evol. 29 (2): 157â€“169. doi:10.1007/BF02100114. PMID 2509716.
- Esposti MD, Crimi M, Ghelli A, Patarnello T, Meyer A, De Vries S (1993). "Mitochondrial cytochrome b: evolution and structure of the protein" (PDF). Biochim. Biophys. Acta. 1143 (3): 243â€“271. doi:10.1016/0005-2728(93)90197-N. PMID 8329437.
- Castresana, J. (2001). "Cytochrome b Phylogeny and the Taxonomy of Great Apes and Mammals". Molecular Biology and Evolution. 18 (4): 465â€“471. doi:10.1093/oxfordjournals.molbev.a003825. PMID 11264397.
- Blakely EL, Mitchell AL, Fisher N, Meunier B, Nijtmans LG, Schaefer AM, Jackson MJ, Turnbull DM, Taylor RW (July 2005). "A mitochondrial cytochrome b mutation causing severe respiratory chain enzyme deficiency in humans and yeast". FEBS J. 272 (14): 3583â€“92. doi:10.1111/j.1742-4658.2005.04779.x. PMID 16008558.
- Siregar JE, Syafruddin D, Matsuoka H, Kita K, Marzuki S (June 2008). "Mutation underlying resistance of Plasmodium berghei to atovaquone in the quinone binding domain 2 (Qo(2)) of the cytochrome b gene". Parasitology International. 57 (2): 229â€“32. doi:10.1016/j.parint.2007.12.002. PMID 18248769.
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Cytochrome b(C-terminal)/b6/petD Provide feedback
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005798
In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III ( EC ) - also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase ( EC ), also known as the b6f complex.
Cytochrome b/b6 [ PUBMED:2509716 , PUBMED:8329437 ] is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two haem groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two haem groups.
Apart from regions around some of the histidine haem ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane. This entry is the C terminus of these proteins.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||electron transfer activity (GO:0009055)|
|oxidoreductase activity (GO:0016491)|
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|Number in seed:||157|
|Number in full:||4277|
|Average length of the domain:||104.80 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||28.49 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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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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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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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 Cytochrom_B_C domain has been found. There are 184 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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