Summary: Cytochrome C'
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This is the Wikipedia entry entitled "Cytochrome c family". More...
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Cytochrome c family Edit Wikipedia article
Structure of cytochrome c2 from Rhodopseudomonas viridis.
atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 angstroms resolution
|Class III cytochrome C family|
sulfate respiration in desulfovibrio vulgaris hildenborough: structure of the 16-heme cytochrome c hmca at 2.5 a resolution and a view of its role in transmembrane electron transfer
Cytochromes c (cytC) are electron-transfer proteins having one or several heme c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. Cytochromes c possess a wide range of properties and function in a large number of different redox processes. The founding member of this family is mitochondrial cytochrome c.
Ambler recognized four classes of cytC.
- Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N-terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C-terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cytc-550, which have several extra loops by comparison with class IB cytC.
- Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding.
- Class III comprises the low redox potential multiple haem cytochromes: cyt C7 (trihaem), C3 (tetrahaem), and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV. The 3D structures of a number of cyt C3 proteins have been determined. The proteins consist of 4-5 alpha-helices and 2 beta-strands wrapped around a compact core of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved.
- Class IV includes complex proteins containing other prosthetic groups besides haem c, such as flavocytochromes c and cytochromes cd.
Human proteins containing this domain
- Miki K, Sogabe S, Uno A, et al. (May 1994). "Application of an automatic molecular-replacement procedure to crystal structure analysis of cytochrome c2 from Rhodopseudomonas viridis". Acta Crystallogr. D. 50 (Pt 3): 271–5. doi:10.1107/S0907444993013952. PMID 15299438.
- Moore GR, Pettigrew GW (1987). : –. Missing or empty
- Ambler RP (1991). "Sequence variability in bacterial cytochromes c". Biochim. Biophys. Acta. 1058 (1): 42–47. doi:10.1016/S0005-2728(05)80266-X. PMID 1646017.
- Kassner RJ (May 1991). "Ligand binding properties of cytochromes c'". Biochim. Biophys. Acta. 1058 (1): 8–12. doi:10.1016/s0005-2728(05)80257-9. PMID 1646027.
- Moore GR (May 1991). "Bacterial 4-alpha-helical bundle cytochromes". Biochim. Biophys. Acta. 1058 (1): 38–41. doi:10.1016/s0005-2728(05)80265-8. PMID 1646016.
- Ren Z, Meyer T, McRee DE (November 1993). "Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 A resolution". J. Mol. Biol. 234 (2): 433–45. doi:10.1006/jmbi.1993.1597. PMID 8230224.
- Coutinho IB, Xavier AV (1994). "Tetraheme cytochromes". Meth. Enzymol. 243: 119–40. doi:10.1016/0076-6879(94)43011-X. PMID 7830606.
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 C' Provide feedback
No Pfam abstract.
Tahirov TH, Misaki S, Meyer TE, Cusanovich MA, Higuchi Y, Yasuoka N; , J Mol Biol 1996;259:467-479.: High-resolution crystal structures of two polymorphs of cytochrome c' from the purple phototrophic bacterium rhodobacter capsulatus. PUBMED:8676382 EPMC:8676382
Internal database links
|Similarity to PfamA using HHSearch:||Cytochrom_B562|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002321
Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [PUBMED:1646017] recognised four classes of cytC.
Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins [PUBMED:1646027]. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein [PUBMED:1646016].
The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core [PUBMED:1646016]. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [PUBMED:8230224].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||electron transfer activity (GO:0009055)|
|heme binding (GO:0020037)|
|iron ion binding (GO:0005506)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. 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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|Seed source:||Sarah Teichmann|
|Author:||Finn RD , Bateman A|
|Number in seed:||141|
|Number in full:||1946|
|Average length of the domain:||113.40 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||72.15 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -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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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
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.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
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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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_C_2 domain has been found. There are 92 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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