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Last modified: 16 March 1999


Class I cytochromes c

Haem type Haem iron coordination Axial iron ligands Formal iron
oxidation/spin
states
Haem c image
Haem c
His-Haem-Met image
Hexacoordinate
NepsilonHis;

SdeltaMet

FeII (S=0);
FeIII (S=1/2)

Cytochromes c (cyt c) can be defined as electron­transfer proteins having one or several haem c groups, bound to the protein by one or, more commonly two, thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. Cyt c possess a wide range of properties and function in a large number of different redox processes [1].

Ambler [2] recognised four classes of cyt c. Class I includes the low­spin soluble cyt c of mitochondria and bacteria, with the haem­attachment site towards the N­terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C­terminus. Most of Class I cyt c contain a single haem c group; cyt c4, bacterial cyt c peroxidase and the cytochrome subunit of flavocytochrome c sulphide dehydrogenase contain two haem c groups [3].

3­D structures of a considerable number of Class I cyt c have been determined [1]. The proteins consist of 3-7 alpha­helices; three most conserved `core' helices form a `basket' around the haem group with one haem edge exposed to the solvent (see Figure 1CRY). The dihaem cytochrome subunit of flavocytochrome c sulphide dehydrogenase contains two domains, each resembling mitochondrial cytochrome c, and has an unusual interpropionic acid linkage joining the two haem groups in the interior of the subunit [4]. Similarly, the dihaem cytochrome c peroxidase from Pseudomonas aeruginosa consists of two Class I cyt c­like domains [5].

Thermodynamic properties of Class I cytochromes c

Protein pH ProTherm
entry
Mutation Method
Cytochrome c2; Rhodobacter capsulatus 7.5 351 wild type GdnHCl
352 K12D GdnHCl
353 K14E GdnHCl
354 K32E GdnHCl
2210 K14E, K32E GdnHCl
Iso­1­cytochrome c; Saccharomyces cerevisiae 7.5 277; 3584 wild type GdnHCl
278 K73M GdnHCl
279 K73Y GdnHCl
280 K73F GdnHCl
281; 3585 K73W GdnHCl
3586 K73V GdnHCl
3587 K73I GdnHCl
6.0 2742 wild type thermal
2743 N57I thermal
2960 wild type thermal
2961 G29S, N52I thermal
2962 H33P, N52I thermal
2963 N52I thermal
2964 C102S thermal
2965 C102A thermal
2966 N52A, C102A thermal
2967 N52G, C102A thermal
2968 N52I, C102A thermal
5.5 3561 K73W thermal
5.25 3560 K73W thermal
5.0 3550 wild type thermal
3559 K73W thermal
3570 K73V thermal
3579 K73I thermal
4.75 3549 wild type thermal
3558 K73W thermal
3569 K73V thermal
3578 K73I thermal
4.6 3510 wild type thermal
3511 P76L thermal
3512 P76G thermal
3513 P76V thermal
3514 P76R thermal
3515 P76S thermal
3516 P76Y thermal
3517 P76W thermal
4.5 3548; 3580 wild type thermal
3557; 3581 K73W thermal
3568; 3582 K73V thermal
3577; 3583 K73I thermal
4.25 3547 wild type thermal
3556 K73W thermal
3567 K73V thermal
3576 K73I thermal
4.0 3546 wild type thermal
3555 K73W thermal
3566 K73V thermal
3575 K73I thermal
3.75 3545 wild type thermal
3554 K73W thermal
3565 K73V thermal
3574 K73I thermal
3.5 3544 wild type thermal
3553 K73W thermal
3564 K73V thermal
3573 K73I thermal
3.25 3543 wild type thermal
3552 K73W thermal
3563 K73V thermal
3572 K73I thermal
3.0 3542 wild type thermal
3551 K73W thermal
3562 K73V thermal
3571 K73I thermal
Iso­2­cytochrome c; Saccharomyces cerevisiae 7.2 3029 wild type GdnHCl
3030 P71T GdnHCl

Class I cytochromes c in motif databases

PRINTS ID PRINTS AC PROSITE/BLOCKS ID PROSITE AC BLOCKS AC
CYTCHRMECIAB PR00604 CYTOCHROME_C PS00190 BL00190
CYTCHROMECIC PR00605
CYTCHROMECID PR00606
CYTCHROMECIE PR00607

Class I cytochromes c in alignment databases

Protein Superfamily Protein Homology Domain Pfam LPFC 3­D alignment
00001; cytochrome c
00002; cytochrome c4
00005; cytochrome c552
03773; Pseudomonas cytochrome c peroxidase
03808; E. coli cytochrome c peroxidase
03823; cytochrome c6
00326; cytochrome c peroxidase
00331; cytochrome c6
PF00034; cytochrome_c
cytc
cyt5

Class I cytochromes c in 3­D databases

All Class I cytochromes c contain single covalently bound haem c group (see
Figure 1CRY) except for * containing two covalently bound haem c groups per cytochrome subunit.

PDB scop BSMRELI
Base
Header MMS Abstract ¹
05c1 05c1
-
-
Cytochrome c555; Chlorobium thiosulfatophilum
-
155c 155c 155c 155c Cytochrome c550; Paracoccus denitrificans
-
1a2s
-
1a2s
-
Cytochrome c6 (syn. cytochrome c552) (oxidised); Monoraphidium braunii
-
1a56
-
1a56
-
Cytochrome c552 (reduced) (NMR, mean structure refined with explicit hydrogen bond constraints); Nitrosomonas europaea
-
1a8c
-
1a8c
-
Cytochrome c552 (reduced) (NMR, mean structure refined without hydrogen bond constraints); Nitrosomonas europaea
-
1akk 1akk 1akk 1akk Cytochrome c (oxidised); horse heart
-
1c2r 1c2r 1c2r 1c2r Cytochrome c2; Rhodobacter capsulatus MMS92042
1c52
-
1c52
-
Cytochrome c552 (oxidised); Thermus thermophilus
-
1c53 1c53 1c53 1c53 Cytochrome c553; Desulfovibrio vulgaris, strain Miyazaki F MMS91032
1c6s
-
1c6s
-
Cytochrome c6 (syn. cytochrome c553) (reduced); Synechococcus elongatus
-
1cc5 1cc5 1cc5 1cc5 Cytochrome c5 (oxidised); Azotobacter vinelandii
-
1cch 1cch 1cch 1cch Cytochrome c551; Pseudomonas stutzeri strain ZoBell
-
1ccr 1ccr 1ccr 1ccr Cytochrome c; rice (Oryza sativa) embryo
-
1ced 1ced 1ced 1ced Cytochrome c6 (syn. cytochrome c552) (reduced); Monoraphidium braunii
-
1chh 1chh 1chh 1chh Cytochrome c (isozyme 1) (reduced) (F82Y, C102T mutant); Saccharomyces cerevisiae
-
1chi 1chi 1chi 1chi Cytochrome c (isozyme 1) (reduced) (F82Y, L85A, C102T mutant); Saccharomyces cerevisiae
-
1chj 1chj 1chj 1chj Cytochrome c (isozyme 1) (reduced) (L85A, C102T mutant); Saccharomyces cerevisiae
-
1cie 1cie 1cie 1cie Cytochrome c (isozyme 1) (reduced) (N52I, F82S, C102A mutant); Saccharomyces cerevisiae
-
1cif 1cif 1cif 1cif Cytochrome c (isozyme 1) (reduced) (R38A, F82S, C102A mutant); Saccharomyces cerevisiae
-
1cig 1cig 1cig 1cig Cytochrome c (isozyme 1) (reduced) (R38A, N52I, C102A mutant); Saccharomyces cerevisiae
-
1cih 1cih 1cih 1cih Cytochrome c (isozyme 1) (reduced) (R38A, N52I, F82S, C102A mutant); Saccharomyces cerevisiae
-
1cor 1cor 1cor 1cor Cytochrome c551; Pseudomonas stutzeri
-
1cot 1cot 1cot 1cot Cytochrome c2 (formerly cytochrome c550); Paracoccus denitrificans
-
1crc 1crc 1crc 1crc Cytochrome c (at low ionic strength); horse heart MS6LBC12
1crg 1crg 1crg 1crg Cytochrome c (isozyme 1) (oxidised) (N52I, C102T mutant); Saccharomyces cerevisiae
-
1crh 1crh 1crh 1crh Cytochrome c (isozyme 1) (reduced) (N52I mutant); Saccharomyces cerevisiae
-
1cri 1cri 1cri 1cri Cytochrome c (isozyme 1) (oxidised) (N52I, Y67F, C102T mutant); Saccharomyces cerevisiae
-
1crj 1crj 1crj 1crj Cytochrome c (isozyme 1) (reduced) (N52I, Y67F, C102T mutant); Saccharomyces cerevisiae
-
1cry 1cry 1cry 1cry Cytochrome c2; Rhodopseudomonas viridis MS5NG9
1csu 1csu 1csu 1csu Cytochrome c (isozyme 1) (reduced) (L85C, C102T mutant); Saccharomyces cerevisiae
-
1csv 1csv 1csv 1csv Cytochrome c (isozyme 1) (reduced) (L85F, C102T mutant); Saccharomyces cerevisiae
-
1csw 1csw 1csw 1csw Cytochrome c (isozyme 1) (reduced) (L85M, C102T mutant); Saccharomyces cerevisiae
-
1csx 1csx 1csx 1csx Cytochrome c (isozyme 1) (reduced) (L94S, C102T mutant); Saccharomyces cerevisiae
-
1ctj 1ctj 1ctj 1ctj Cytochrome c6; Monoraphidium braunii MS6WH4
1cty 1cty 1cty 1cty Cytochrome c (isozyme 1) (oxidised) (Y67F, C102T mutant); Saccharomyces cerevisiae
-
1ctz 1ctz 1ctz 1ctz Cytochrome c (isozyme 1) (reduced) (Y67F, C102T mutant); Saccharomyces cerevisiae
-
1cxa 1cxa 1cxa 1cxa Cytochrome c2 (complex with imidazole; hexagonal form); Rhodobacter sphaeroides MS5DR5
1cxc 1cxc 1cxc 1cxc Cytochrome c2 (tetragonal form); Rhodobacter sphaeroides MS5DR7
1cyc 1cyc 1cyc 1cyc Cytochrome c (reduced); Bonito (Katsuwonus pelamis)
-
1cyi 1cyi 1cyi 1cyi Cytochrome c6 (cytochrome c553) (complex with Cd2+); Chlamydomonas reinhardtii MS6MR3
1cyj 1cyj 1cyj 1cyj Cytochrome c6 (cytochrome c553) (complex with Cd2+); Chlamydomonas reinhardtii MS6MR3
1dvh 1dvh 1dvh 1dvh Cytochrome c553 (reduced); Desulfovibrio vulgaris MS6KSC1
1etp* 1etp* 1etp* 1etp* Cytochrome c4; Pseudomonas stutzeri
-
1fcd* 1fcd* 1fcd* 1fcd* Flavocytochrome c sulphide dehydrogenase (FCSD); Chromatium vinosum MS5MM11*
1fhb 1fhb 1fhb 1fhb Cytochrome c (isozyme 1) (oxidised) (cyanide adduct of A80) (H39Q, M80A, C102S mutant); Saccharomyces cerevisiae
-
1giw
-
1giw
-
Cytochrome c (reduced); horse heart
-
1gks 1gks 1gks 1gks Cytochrome c551 (reduced); Ectothiorhodospira halophila MS7RBC1
1hrc 1hrc 1hrc 1hrc Cytochrome c; horse heart
-
1hro 1hro 1hro 1hro High­potential cytochrome c2; Rhodopila globiformis
-
1irv 1irv 1irv 1irv Cytochrome c (isozyme 1) (reduced) (complex with sulphate) (I75M, C102T mutant, methylated Lys­72); Saccharomyces cerevisiae
-
1irw 1irw 1irw 1irw Cytochrome c (isozyme 1) (reduced) (complex with sulphate) (N52A, C102T mutant, methylated Lys­72); Saccharomyces cerevisiae
-
1ocd 1ocd 1ocd 1ocd Cytochrome c (oxidised); horse heart
-
1rap 1rap 1rap 1rap Rep A2 iso­1­cytochrome c (reduced) (E21D, K22Q, P25A, H26N mutant); Saccharomyces cerevisiae
-
1raq 1raq 1raq 1raq Rep A2 iso­1­cytochrome c (reduced) (E21D, K22Q, P25A, H26N mutant); Saccharomyces cerevisiae
-
1ycc 1ycc 1ycc 1ycc Cytochrome c (isozyme 1) (reduced); Saccharomyces cerevisiae
-
1yea 1yea 1yea 1yea Cytochrome c (iso­2) (reduced); Saccharomyces cerevisiae
-
1yeb 1yeb 1yeb 1yeb Cytochrome c (B­2036 composite) (reduced); Saccharomyces cerevisiae
-
1yfc 1yfc 1yfc 1yfc Cytochrome c (iso­1) (reduced) (C102S mutant, methylated Lys­72); Saccharomyces cerevisiae MS7GA6
1yic 1yic 1yic 1yic Cytochrome c (iso­1) (oxidised) (C102S mutant, methylated Lys­72); Saccharomyces cerevisiae
-
1ytc 1ytc 1ytc 1ytc Cytochrome c (iso­2); Saccharomyces cerevisiae
-
2c2c 2c2c 2c2c 2c2c Cytochrome c2 (oxidised); Rhodospirillum rubrum
-
2cxb 2cxb 2cxb 2cxb Cytochrome c2 (triclinic form); Rhodobacter sphaeroides MS5DR6
2dvh 2dvh 2dvh 2dvh Cytochrome c553 (Y64A mutant); Desulfovibrio vulgaris Hildenborough
-
2frc 2frc 2frc 2frc Cytochrome c (reduced); horse heart MS5KS17
2giw
-
2giw
-
Cytochrome c (reduced); horse heart
-
2mta 2mta 2mta 2mta Methylamine dehydrogenase complex with amicyanin and cytochrome c551i; Paracoccus denitrificans MS5TL2
2pac 2pac 2pac 2pac Cytochrome c551; Pseudomonas aeruginosa MMS92044
2pcb 2pcb 2pcb 2pcb Yeast cytochrome c peroxidase (CCP) complex with horse heart cytochrome c MMS93043
2pcc 2pcc 2pcc 2pcc Yeast cytochrome c peroxidase (CCP) complex with yeast iso­1­cytochrome c; Saccharomyces cerevisiae MMS93044
2ycc 2ycc 2ycc 2ycc Cytochrome c (isozyme 1) (oxidised) (C102T mutant); Saccharomyces cerevisiae
-
351c 351c 351c 351c Cytochrome c551 (oxidised); Pseudomonas aeruginosa
-
3c2c 3c2c 3c2c 3c2c Cytochrome c2 (reduced); Rhodospirillum rubrum
-
3cyt 3cyt 3cyt 3cyt Cytochrome c (oxidised); albacore tuna (Thunnus alalunga) heart
-
451c 451c 451c 451c Cytochrome c551 (reduced); Pseudomonas aeruginosa
-
5cyt 5cyt 5cyt 5cyt Cytochrome c (reduced); albacore tuna (Thunnus alalunga) heart
-
-
s005
-
-
Di­haem cytochrome c peroxidase; Pseudomonas aeruginosa MS6DT11

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

  1. Pettigrew, G.W. and Moore, G.R. (1987) Cytochromes c. Biological Aspects. Springer­Verlag, Berlin - Heidelberg - New York.
  2. Ambler, R.P. (1991) Sequence variability in bacterial cytochromes c. Biochim. Biophys. Acta 1058, 42-47.
  3. van Beeumen, J. (1991) Primary structure diversity of prokaryotic diheme cytochromes c. Biochim. Biophys. Acta 1058, 56-60.
  4. Chen, Z.­W., Koh, M., van Driessche, G., van Beeumen, J.J., Bartsch, R.G., Meyer, T.E., Cusanovich, M.A. and Mathews, F.S. (1994) The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Science 266, 430-432.
  5. Fülöp, V., Ridout, C.J., Greenwood, C. and Hajdu, J. (1995) Crystal structure of the di­haem cytochrome c peroxidase from Pseudomonas aeruginosa. Structure 3, 1225-1233.
Bibliography on structural studies of Class I cytochromes c