Summary: Cytochrome b(N-terminal)/b6/petB
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Cytochrome b Edit Wikipedia article
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Mitochondrial cytochrome bc1 complex
In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (EC 126.96.36.199) - 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, pumping of protons to the create a PMF. The proton gradient is finally used for the generation of ATP. Concluding, the complexes play a vital part 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 to determine 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 deepen the understanding of evolutionary relationships.
Human genes encoding cytochrome b proteins include:
- CYB5A – cytochrome b5 type A (microsomal)
- CYB5B – cytochrome b5 type B (outer mitochondrial membrane)
- CYBASC3 – cytochrome b, ascorbate dependent 3
- MT-CYB – mitochondrially encoded cytochrome b
- Howell N (August 1989). "Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis". J. Mol. Evol. 29 (2): 157–69. 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". Biochim. Biophys. Acta 1143 (3): 243–71. doi:10.1016/0005-2728(93)90197-N. PMID 8329437.
- Blankenship, Robert (2009). Molecular Mechanisms of Photosynthesis. Blackwell Publishing. pp. 124–132.
- 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): 157–169. 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". Biochim. Biophys. Acta 1143 (3): 243–271. 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): 465–471. 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): 3583–92. 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): 229–32. doi:10.1016/j.parint.2007.12.002. PMID 18248769.
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This superfamily includes a variety of different heme binding cytochromes.
The clan contains the following 10 members:COX15-CtaA Cytochrom_B561 Cytochrom_B_N Cytochrom_B_N_2 Cytochrom_C_asm DUF2427 DUF4405 Ferric_reduct Ni_hydr_CYTB PCRF
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Curation and family details
|Number in seed:||68|
|Number in full:||102102|
|Average length of the domain:||142.10 aa|
|Average identity of full alignment:||66 %|
|Average coverage of the sequence by the domain:||51.21 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
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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_N_2 domain has been found. There are 95 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 seqence.
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