Summary: Cytochrome b/b6/petB
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Cytochrome b Edit Wikipedia article
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 Mitochondrial cytochrome bc1 complex | |||||||||
| Identifiers | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Symbol | Cytochrom_B_N | ||||||||
| Pfam | PF00033 | ||||||||
| InterPro | IPR005797 | ||||||||
| PROSITE | PDOC00171 | ||||||||
| SCOPe | 3bcc / SUPFAM | ||||||||
| TCDB | 3.D.3 | ||||||||
| OPM superfamily | 3 | ||||||||
| OPM protein | 3h1j | ||||||||
| CDD | cd00284 | ||||||||
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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.[1][2]
Contents
Function
In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (EC 1.10.2.2) — 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 1.10.99.1), 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.[3]
Structure
Cytochrome b/b6[4][5] 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.[6]
Clinical significance
Mutations in cytochrome b primarily result in exercise intolerance in human patients; though more rare, severe multi-system pathologies have also been reported.[7]
Single-point mutations in cytochrome b of Plasmodium falciparum and P. berghei are associated with resistance to the anti-malarial drug atovaquone.[8]
Human genes
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
References
- ^ 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): 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" (PDF). 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" (PDF). 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.
External links
- Cytochromes+b at the US National Library of Medicine Medical Subject Headings (MeSH)
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Cytochrome b/b6/petB Provide feedback
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Internal database links
| SCOOP: | Cytochrom_B_N_2 DUF4405 Ni_hydr_CYTB |
| Similarity to PfamA using HHSearch: | Cytochrom_B_N_2 |
External database links
| HOMSTRAD: | cytochrome_b |
| PROSITE: | PDOC00171 |
| SCOP: | 3bcc |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005797
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 represents the N-terminal region of these proteins.
Gene Ontology
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) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan 2heme_cytochrom (CL0328), which has the following description:
This superfamily includes a variety of different heme binding cytochromes.
The clan contains the following 9 members:
COX15-CtaA Cytochrom_B561 Cytochrom_B_N_2 Cytochrom_C_asm Cytochrome_B DUF2427 DUF4405 Ferric_reduct Ni_hydr_CYTBAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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| Seed (8) |
Full (3728) |
Representative proteomes | UniProt (224023) |
NCBI (230620) |
Meta (2675) |
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| RP15 (486) |
RP35 (1767) |
RP55 (3652) |
RP75 (5943) |
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| HTML | |||||||||
| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (8) |
Full (3728) |
Representative proteomes | UniProt (224023) |
NCBI (230620) |
Meta (2675) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (486) |
RP35 (1767) |
RP55 (3652) |
RP75 (5943) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
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.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | Prosite |
| Previous IDs: | cytochrome_b_N; Cytochrom_B_N; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Sonnhammer ELL 
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| Number in seed: | 8 |
| Number in full: | 3728 |
| Average length of the domain: | 183.10 aa |
| Average identity of full alignment: | 45 % |
| Average coverage of the sequence by the domain: | 49.08 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 189 | ||||||||||||
| Family (HMM) version: | 20 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Interactions
Structures
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 Cytochrome_B domain has been found. There are 173 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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