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95  structures 28713  species 9  interactions 70433  sequences 20  architectures

Family: Cytochrom_B_C (PF00032)

Summary: Cytochrome b(C-terminal)/b6/petD

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This is the Wikipedia entry entitled "Cytochrome b". More...

Cytochrome b Edit Wikipedia article

1l0l opm.gif
Identifiers
Symbol Cytochrom_B_N
Pfam PF00033
InterPro IPR005797
PROSITE PDOC00171
SCOP 3bcc
SUPERFAMILY 3bcc
TCDB 3.D.3
OPM superfamily 3
OPM protein 3h1j
CDD cd00284

Cytochrome b is the main subunit of transmembrane cytochrome bc1 and b6f complexes.[1][2]

Function[edit]

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, 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.[3]

Structure[edit]

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[edit]

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.[6]

Clinical significance[edit]

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[edit]

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[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ Blankenship, Robert (2009). Molecular Mechanisms of Photosynthesis. Blackwell Publishing. pp. 124–132. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ Castresana, J. (2001). "Cytochrome b Phylogeny and the Taxonomy of Great Apes and Mammals". Molecular Biology and Evolution 18 (4): 465–471. PMID 11264397. 
  7. ^ 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. 
  8. ^ 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[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome b(C-terminal)/b6/petD Provide feedback

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Literature references

  1. Zhang Z, Huang L, Shulmeister VM, Chi YI, Kim KK, Hung LW, Crofts AR, Berry EA, Kim SH; , Nature 1998;392:677-684.: Electron transfer by domain movement in cytochrome bc1. PUBMED:9565029 EPMC:9565029


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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(114)
Full
(70433)
Representative proteomes NCBI
(68332)
Meta
(2102)
RP15
(158)
RP35
(359)
RP55
(481)
RP75
(599)
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Format an alignment

  Seed
(114)
Full
(70433)
Representative proteomes NCBI
(68332)
Meta
(2102)
RP15
(158)
RP35
(359)
RP55
(481)
RP75
(599)
Alignment:
Format:
Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(114)
Full
(70433)
Representative proteomes NCBI
(68332)
Meta
(2102)
RP15
(158)
RP35
(359)
RP55
(481)
RP75
(599)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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

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Seed source: Prosite
Previous IDs: cytochrome_b_C;
Type: Domain
Author: Sonnhammer ELL
Number in seed: 114
Number in full: 70433
Average length of the domain: 89.80 aa
Average identity of full alignment: 73 %
Average coverage of the sequence by the domain: 27.89 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 18.9
Trusted cut-off 20.7 19.3
Noise cut-off 20.6 18.8
Model length: 102
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 9 interactions for this family. More...

PetM Cytochrom_C1 UcrQ PetG Apocytochr_F_C Cytochrom_B_C UCR_14kD Rieske Cytochrom_B_N

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 Cytochrom_B_C 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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