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53  structures 492  species 1  interaction 629  sequences 2  architectures

Family: Cytochrom_C_2 (PF01322)

Summary: Cytochrome C'

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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]
Identifiers
Symbol Cytochrom_C
Pfam PF00034
InterPro IPR003088
PROSITE PDOC00169
SCOP 1cry
SUPERFAMILY 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
Identifiers
Symbol Cytochrom_C_2
Pfam PF01322
InterPro IPR002321
PROSITE PDOC00169
SCOP 1cgo
SUPERFAMILY 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
Identifiers
Symbol Cytochrom_CIII
Pfam PF02085
Pfam clan CL0317
InterPro IPR020942
SCOP 2cdv
SUPERFAMILY 2cdv

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]

Subfamilies[edit]

Human proteins containing this domain[edit]

CYCS;

References[edit]

  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 Biol. Crystallogr. 50 (Pt 3): 271–5. doi:10.1107/S0907444993013952. PMID 15299438. 
  2. ^ Moore GR, Pettigrew GW (1987). pp. –.  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. PMID 1646027. 
  5. ^ a b Moore GR (May 1991). "Bacterial 4-alpha-helical bundle cytochromes". Biochim. Biophys. Acta 1058 (1): 38–41. 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. Ren Z, Meyer T, McRee DE; , J Mol Biol 1993;234:433-445.: Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 A resolution. PUBMED:8230224 EPMC:8230224

  2. 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


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].

Gene Ontology

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Domain organisation

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Alignments

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(648)
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(813)
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(144)
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RP75
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  Seed
(95)
Full
(629)
Representative proteomes NCBI
(648)
Meta
(813)
RP15
(54)
RP35
(144)
RP55
(186)
RP75
(234)
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  Seed
(95)
Full
(629)
Representative proteomes NCBI
(648)
Meta
(813)
RP15
(54)
RP35
(144)
RP55
(186)
RP75
(234)
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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 View help on the curation process

Seed source: Sarah Teichmann
Previous IDs: Cytochrome_C_2;
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 95
Number in full: 629
Average length of the domain: 114.10 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 73.21 %

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 21.2 21.2
Trusted cut-off 21.3 21.2
Noise cut-off 21.1 21.1
Model length: 122
Family (HMM) version: 15
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Species distribution

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Interactions

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Cytochrom_C_2

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_C_2 domain has been found. There are 53 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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