SUPERFAMILY 1.73 HMM library and genome assignments server


Cytochrome c superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (258)
Fold:   Cytochrome c [ 46625]
  core: 3 helices; folded leaf, opened
Superfamily:   Cytochrome c [ 46626] (8)
Families:   monodomain cytochrome c [ 46627] (15)
  N-terminal (heme c) domain of cytochrome cd1-nitrite reductase [ 46671]
  Quinoprotein alcohol dehydrogenase, C-terminal domain [ 68952]
  Cytochrome bc1 domain [ 46676]
  Two-domain cytochrome c [ 46680] (2)
  duplication: consists of two cytochrome c type domains
  Di-heme cytochrome c SoxA [ 81677]
  two-domain cytochrome c with novel domain arrangement
  Di-heme cytochrome c peroxidase [ 46685]
  duplication: contains two cytochrome c-type domains
  Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 [ 68956]


Superfamily statistics
Genomes (885) UniProt 15.0 PDB chains (SCOP 1.73)
Domains 9,433 13,752 118
Proteins 6,985 10,147 109


Functional annotation
General category Metabolism
Detailed category E- transfer

Function annotation of SCOP domain superfamilies
InterPro annotation
Cross references IPR009056 SSF46626 Protein matches
Abstract

After cytochrome c is synthesized in the cytoplasm as apocytochrome c, it is transported through the outer mitochondrial membrane to the intermembrane space, where haem is covalently attached by thioester bonds to two cysteine residues located in the cytochrome c centre. Cytochrome c is required during oxidative phosphorylation as an electron shuttle between Complex III (cytochrome c reductase) and IV (cytochrome c oxidase). In addition, cytochrome c is involved in apoptosis in more complex organisms such as Xenopus, rats and humans. Cellular stress can induce cytochrome c release from the mitochondrial membrane. In mammals, cytochrome c triggers the assembly of the apoptosome, consisting of cytochrome c, Apaf-1 and dATP, which activates caspase-9, leading to cell death [PubMed12729583, PubMed10707095]. There are several different members of the cytochrome c family with different functional roles, for instance cytochrome c549 is associated with photosystem II [PubMed11315568].

The known structures of c-type cytochromes have six different classes of fold. Of these, four are unique to c-type cytochromes [PubMed12594933, PubMed2166169]. The consensus sequence for the cytochrome c centre is Cys-X-X-Cys-His, where the histidine residue is one of the two axial ligands of the haem iron [PubMed10647174]. This arrangement is shared by all proteins known to belong to the cytochrome c family, which presently includes both mono-haem proteins and multi-haem proteins. This entry represents mono-haem cytochrome c proteins (excluding class II and f-type cytochromes), such as cytochromes c, c1, c2, c5, c555, c550 to c553, c556, and c6.

Cytochrome c-type centres are also found in the active sites of many enzymes, including cytochrome cd1-nitrite reductase as the N-terminal haem c domain, in quinoprotein alcohol dehydrogenase as the C-terminal domain, in Quinohemoprotein amine dehydrogenase A chain as domains 1 and 2, and in the cytochrome bc1 complex as the cytochrome bc1 domain.


InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 72 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Cytochrome c domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 72 hidden Markov models representing the Cytochrome c superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Internal database links ]