| Literature References | 1. PETTIGREW, G.W. AND MOORE, G.R.
Cytochromes c. Biological Aspects.
SPRINGER-VERLAG, BERLIN-HEIDELBERG-NEW YORK (1987).
2. AMBLER, R.P.
Sequence variability in bacterial cytochromes c.
BIOCHIM.BIOPHYS.ACTA 1058 42-47 (1991).
3. KERFELD, C.A., ANWAR, H.P., INTERRANTE, R., MERCHANT, S. AND YEATES, T.O.
The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence
for functional oligomerization.
J.MOL.BIOL. 250 627-647 (1995).
4. NAKAGAWA, A., HIGUCHI, Y., YASUOKA, N., KATSUBE, Y. AND YAGI, T.
S-class cytochromes c have a variety of folding patterns: structure of
cytochrome c-553 from Desulfovibrio vulgaris determined by the
multi-wavelength anomalous dispersion method.
J.BIOCHEMISTRY 108 701-703 (1990).
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| Documentation | Cytochromes c (cyt c) 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. 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 low-spin
soluble cyt c 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 cyt c were further subdivided into five
classes, IA to IE. Class IC, "split-alpha-band" cyt c, possess a widened
or split alpha-band of lowered absorptivity. This class includes dihaem
cyt c4 and monohaem cyt c6 (cyt c-553) and cyt c-554.
The 3D structures of Chlamydomonas reinhardtii cyt c6 [3] and Desulfovibrio
vulgaris cyt c-553 [4] have been determined. The proteins consist of 4
alpha-helices; three "core" helices form a "basket" around the haem group,
with one haem edge exposed to the solvent.
CYTCHROMECIC is a 2-element fingerprint that provides a signature for the
class IC cyt c. The fingerprint was derived from an initial alignment of 17
sequences: motif 1 is situated in the loop between helices 1 and 2, and
includes two invariant Cys residues, which covalently bind the haem group,
and a His residue, which provides the fifth haem iron ligand (cf. PROSITE
pattern CYTOCHROME_C); and motif 2 includes both an invariant Met, which
provides the sixth haem iron ligand, and the N-terminal part of helix 4,
which contains a conserved aromatic residue. Two iterations on OWL28.0 were
required to reach convergence, at which point a true set comprising 41
sequences was identified.
An update on SPTR37_9f identified a true set of 50 sequences.
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| Sequence Titles | C553_DESDN CYTOCHROME C-553 (C553) - DESULFOVIBRIO DESULFURICANS (STRAIN NORWAY 4).
C553_DESVH CYTOCHROME C-553 PRECURSOR (C553) (LOW POTENTIAL CYTOCHROME C) - DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH).
C553_DESVM CYTOCHROME C-553 PRECURSOR (C553) - DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI).
C554_PARSP CYTOCHROME C-554(548) (C554) - PARACOCCUS SP. (STRAIN ATCC 12084).
C554_THINE CYTOCHROME C-554(547) (C554) - THIOBACILLUS NEAPOLITANUS.
COX2_BACSU CYTOCHROME C OXIDASE POLYPEPTIDE II PRECURSOR (EC 1.9.3.1) (CYTOCHROME AA3 SUBUN
CYC4_AZOVI CYTOCHROME C4 PRECURSOR - AZOTOBACTER VINELANDII.
CYC4_PSEAE CYTOCHROME C4 - PSEUDOMONAS AERUGINOSA.
CYC4_PSEST CYTOCHROME C4 PRECURSOR - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
CYC6_ALAES CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ALARIA ESCULENTA (ATLANTIC WAKAME) (BADDERLOCKS).
CYC6_ANANI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANACYSTIS NIDULANS.
CYC6_ANASP CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA SP. (STRAIN PCC 7120).
CYC6_ANASQ CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA SP. (STRAIN PCC 7937).
CYC6_ANAVA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA VARIABILIS.
CYC6_APHFL CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - APHANIZOMENON FLOS-AQUAE.
CYC6_BRYMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BRYOPSIS MAXIMA.
CYC6_BUMFI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BUMILLERIOPSIS FILIFORMIS.
CYC6_CHLRE CYTOCHROME C6 PRECURSOR (CYTOCHROME C552) - CHLAMYDOMONAS REINHARDTII.
CYC6_EUGGR CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUGLENA GRACILIS.
CYC6_EUGVI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUGLENA VIRIDIS.
CYC6_MICAE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - MICROCYSTIS AERUGINOSA.
CYC6_MONBR CYTOCHROME C6 (CYTOCHROME C552) - MONORAPHIDIUM BRAUNII.
CYC6_MONLU CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PAVLOVA LUTHERII (MONOCHRYSIS LUTHERI).
CYC6_PETFA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PETALONIA FASCIA (KELP).
CYC6_PLEBO CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PLECTONEMA BORYANUM.
CYC6_PORPU CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PORPHYRA PURPUREA.
CYC6_PORTE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PORPHYRA TENERA.
CYC6_SPIMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SPIRULINA MAXIMA.
CYC6_SYNEN CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS ELONGATUS NAEGELI.
CYC6_SYNLI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS LIVIDUS.
CYC6_SYNP2 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. (STRAIN PCC 7002) (AGMENELLUM QUADRUPLICATUM).
CYC6_SYNP7 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
CYC6_SYNSP CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP.
CYC6_SYNY3 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
CYCA_ACEPO ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR - ACETOBACTER POLYOXOGENES, AND ACETOBACTER EUROPAEUS.
CYCA_GLUSU ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR (CYTOCHROME C- 553) (C553) (G3-ADH SUBUNIT II) - GLUCONOBACTER SUBOXYDANS.
CYSD_CHLLT CYTOCHROME SUBUNIT OF SULFIDE DEHYDROGENASE (FC) (FCSD) (FLAVOCYTOCHROME C CYTOCHROME SUBUNIT) - CHLOROBIUM LIMICOLA F.SP. THIOSULFATOPHILUM.
O30730 DI-HEME CYTOCHROME CP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O34215 CYTOCHROME C PRECURSOR - ERWINIA CYPRIPEDII.
O34404 CYTOCHROME C OXIDASE POLYPEPTIDE II (EC 1.9.3.1) - BACILLUS SUBTILIS.
O69780 DI-HEME CYTOCHROME C - RHIZOBIUM ETLI.
P72287 FIXPC - RHIZOBIUM LEGUMINOSARUM.
Q03075 CYTOCHROME C - BRADYRHIZOBIUM JAPONICUM.
Q05577 FIXP PROTEIN - RHIZOBIUM MELILOTI.
Q43945 GENES FIXN, FIXO, FIXQ, FIXP AND FIXG - AZORHIZOBIUM CAULINODANS.
Q46444 QUINOHAEMOPROTEIN ETHANOL DEHYDROGENASE TYPE I PRECURSOR (EC 1.1.99.-) (QH-EDH1) - COMAMONAS TESTOSTERONI (PSEUDOMONAS TESTOSTERONI).
Q51682 CCOP - PARACOCCUS DENITRIFICANS.
Q52689 CCOP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
Q53114 CBB3-TYPE CYTOCHROME C OXIDASE CCOP SUBUNIT - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
Q57536 CYTOCHROME C SUBUNIT OF ALCOHOL DEHYDROGENASE - ACETOBACTER PASTEURIANUS.
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