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38  structures 459  species 3  interactions 910  sequences 53  architectures

Family: Cytochrom_c3_2 (PF14537)

Summary: Cytochrome c3

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This is the Wikipedia entry entitled "Cytochrome c family". More...

Cytochrome c family Edit Wikipedia article

Cytochrome c
PDB 1cry EBI.jpg
Structure of cytochrome c2 from Rhodopseudomonas viridis.[1]
Symbol Cytochrom_C
Pfam PF00034
InterPro IPR003088
SCOP 1cry
OPM superfamily 78
OPM protein 1hrc
Cytochrome C'
PDB 1bbh EBI.jpg
atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 angstroms resolution
Symbol Cytochrom_C_2
Pfam PF01322
InterPro IPR002321
SCOP 1cgo
Class III cytochrome C family
PDB 1h29 EBI.jpg
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
Symbol Cytochrom_CIII
Pfam PF02085
Pfam clan CL0317
InterPro IPR020942
SCOP 2cdv
CDD cd08168

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.[2] The founding member of this family is mitochondrial cytochrome c.

Ambler[3] 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.[4] 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.[5] 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.[5] The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding.[6]
  • 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.[7] 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.[7]
  • Class IV includes complex proteins containing other prosthetic groups besides haem c, such as flavocytochromes c and cytochromes cd.[3]


Human proteins containing this domain



  1. ^ 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. 
  2. ^ Moore GR, Pettigrew GW (1987). : –.  Missing or empty |title= (help)
  3. ^ a b 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. 
  4. ^ 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. 
  5. ^ a b 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. 
  6. ^ 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. 
  7. ^ a b Coutinho IB, Xavier AV (1994). "Tetraheme cytochromes". Meth. Enzymol. 243: 119–40. doi:10.1016/0076-6879(94)43011-X. PMID 7830606. 

This article incorporates text from the public domain Pfam and InterPro IPR002321

This article incorporates text from the public domain Pfam and InterPro IPR020942

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.

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Literature references

  1. Gordon EH, Pike AD, Hill AE, Cuthbertson PM, Chapman SK, Reid GA;, Biochem J. 2000;349:153-158.: Identification and characterization of a novel cytochrome c(3) from Shewanella frigidimarina that is involved in Fe(III) respiration. PUBMED:10861223 EPMC:10861223

  2. Leys D, Meyer TE, Tsapin AS, Nealson KH, Cusanovich MA, Van Beeumen JJ;, J Biol Chem. 2002;277:35703-35711.: Crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c. PUBMED:12080059 EPMC:12080059

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012286

Flavocytochrome C3 (Fcc3) enzymes from a number of Shewanella species, including Shewanella frigidimarina (strain NCIMB 400), have respiratory fumarate reductase activity, which enables the bacteria to respire anaerobically with fumarate as a terminal electron acceptor. Flavocytochrome C3 in S. frigidimarina is a soluble, single chain tetrahaem enzyme found in the periplasm, making it distinct from other bacterial fumarate reductases (INTERPRO), which are membrane-bound, multi-subunit enzymes, even though their function is analogous.

Shewanella Fcc3 is composed of three domains: an N-terminal tetrahaem cytochrome domain, a flavin domain and a clamp domain. The cytochrome domain can also occur on its own in some tetrahaem cytochromes implicated in iron oxidation. This entry represents the cytochrome domain, which has a different arrangement of the polypeptide chain in comparison to classical tetra-haem cytochrome C3 [PUBMED:12080059, PUBMED:15581639].

Domain organisation

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Pfam Clan

This family is a member of clan Multiheme_cytos (CL0317), which has the following description:

This family includes cytochromes that contain multiple CxxCH motifs.

The clan contains the following 15 members:

C_GCAxxG_C_C CytoC_RC Cytochrom_c3_2 Cytochrom_C552 Cytochrom_CIII Cytochrom_NNT Cytochrome_C554 Cytochrome_C7 Cytochrome_cB GSu_C4xC__C2xCH Multi-haem_cyto NapB Paired_CXXCH_1 zf-3CxxC zf-3CxxC_2


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Curation and family details

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Seed source: Jackhmmer:Q8EDL6
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 49
Number in full: 910
Average length of the domain: 91.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 28.12 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 80
Family (HMM) version: 6
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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There are 3 interactions for this family. More...

Cytochrom_c3_2 FAD_binding_2 FAD_binding_2


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_c3_2 domain has been found. There are 38 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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