WORKLIST ENTRIES (1):
CYTCHROMECII View alignment View Structure Class II cytochrome C signature
Type of fingerprint: COMPOUND with 2 elements
Links:
PRINTS; PR00603 CYTOCHROMEC1; PR00604 CYTCHRMECIAB; PR00605 CYTCHROMECIC
PRINTS; PR00606 CYTCHROMECID; PR00607 CYTCHROMECIE; PR00609 CYTOCHROMEC3
PRINTS; PR00610 CYTOCHROMEF
INTERPRO; IPR002321
PROSITE; PS00190 CYTOCHROME_C
PFAM; PF01322 Cytochrome_C_2
PDB; 1BBH 3Dinfo; 1CGN 3Dinfo; 2CCY 3Dinfo
SCOP; 1BBH; 1CGN; 2CCY
CATH; 1BBH; 2CCY
Creation date 03-JUL-1996; UPDATE 14-JUN-1999
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. KASSNER, R.J.
Ligand binding properties of cytochromes c'.
BIOCHIM.BIOPHYS.ACTA 1058 8-12 (1991).
4. MOORE, G.R.
Bacterial 4-alpha-helical bundle cytochromes.
BIOCHIM.BIOPHYS.ACTA 1058 38-41 (1991).
5. REN, Z., MEYER, T.E. AND MCREE, D.E.
Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer
dissociation at 1.8A resolution.
J.MOL.BIOL. 234 433-445 (1993).
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 II includes the
high-spin cyt c' and a number of low-spin cytochromes, e.g. cyt c-556.
The haem-attachment site is close to the C-terminus. The cyt c' 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
[3]; this, coupled with its relatively low redox potential, makes it
unlikely that cyt c' is a terminal oxidase. Thus cyt c' probably functions
as an electron transfer protein [4].
The 3D structures of a number of cyt c' 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 [4]. The Chromatium
vinosum cyt c' exhibits dimer dissociation upon ligand binding [5].
CYTCHROMECII is a 2-element fingerprint that provides a signature for the
class II cyt c. The fingerprint was derived from an initial alignment of
17 sequences: the motifs were drawn from adjacent conserved regions in
the C-terminal part of the molecule - motif 2 includes two invariant Cys
residues, which covalently bind the haem group, and a His residue, which
provides the haem iron axial ligand (cf. PROSITE pattern CYTOCHROME_C).
Two iterations on OWL28.0 were required to reach convergence, at which
point a true set comprising 19 sequences was identified.
An update on SPTR37_9f identified a true set of 17 sequences.
SUMMARY INFORMATION
17 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
2| 17 17
--+-----------
| 1 2
True positives..
CYCP_RHOCA CYCP_RHOTE CYCP_RHOSP CYCP_RHOPH
CYCP_RHORU CYCP_ALCSP CYCP_CHRVI C556_AGRTC
C554_RHOSH CYCP_RHOGE CYCP_RHOFU CYCP_RHOMO
C556_AGRTA CYCP_RHOSH C556_AGRTB CYCP_RHOPA
C556_RHOPA
PROTEIN TITLES
CYCP_RHOCA CYTOCHROME C' - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAP
CYCP_RHOTE CYTOCHROME C' - RHODOCYCLUS TENUIS (RHODOSPIRILLUM TENUE).
CYCP_RHOSP CYTOCHROME C' - RHODOPSEUDOMONAS SP.
CYCP_RHOPH CYTOCHROME C' - RHODOSPIRILLUM PHOTOMETRICUM.
CYCP_RHORU CYTOCHROME C' - RHODOSPIRILLUM RUBRUM.
CYCP_ALCSP CYTOCHROME C' - ALCALIGENES SP. (STRAIN NCIB 11015).
CYCP_CHRVI CYTOCHROME C' PRECURSOR - CHROMATIUM VINOSUM.
C556_AGRTC CYTOCHROME C-556 (C556) - AGROBACTERIUM TUMEFACIENS (STRAIN
C554_RHOSH CYTOCHROME C-554 PRECURSOR (C554) (HIGH POTENTIAL CYTOCHROME
CYCP_RHOGE CYTOCHROME C' - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GE
CYCP_RHOFU CYTOCHROME C' - RHODOSPIRILLUM FULVUM.
CYCP_RHOMO CYTOCHROME C' - RHODOSPIRILLUM MOLISCHIANUM.
C556_AGRTA CYTOCHROME C-556 (C556) - AGROBACTERIUM TUMEFACIENS (STRAIN
CYCP_RHOSH CYTOCHROME C' - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SP
C556_AGRTB CYTOCHROME C-556 (C556) - AGROBACTERIUM TUMEFACIENS (STRAIN
CYCP_RHOPA CYTOCHROME C' - RHODOPSEUDOMONAS PALUSTRIS.
C556_RHOPA CYTOCHROME C-556 (C556) - RHODOPSEUDOMONAS PALUSTRIS.
SCAN HISTORY
OWL28_0 2 150 NSINGLE
SPTR37_9f 2 200 NSINGLE
INITIAL MOTIF SETS
CYTCHROMECII1 Length of motif = 24 Motif number = 1
Class II cytochrome c motif I - 1
PCODE ST INT
ANELAKVAATGDAAAVKAQFGKVG CYCP_RHOTE 96 96
GAEVIAAANAGDATAFGAALQKLG CYCP_RHOCA 92 92
ALELASAAETGDKAAIGAKLQALG CYCP_RHORU 90 90
IVKLSAAADAGDLDKLRAAFGDVG CYCP_ALCSP 90 90
AKALAQAATAGDTAQMGKALAALG CYCP_RHOPH 90 90
ANTLAEVAATGEAEAVKTAFGDVG CYCP_CHRVI 95 95
VDKLDAAGKTGDFAQIKAAVGETG CYCP_RHOGE 93 93
GMELIAAANTGEASAFGPALKKLG CYCP_RHOSP 91 91
ESTKLAAAAKAGPDALKAQAAATG CYCP_RHOFU 92 92
ESTKLAAAAKAGPDALKAQAAATG CYCP_RHOMO 92 92
DADKVLASLPADQAGVTAAMQTLG C556_AGRTC 85 85
DADIVLANLPGDQAGVATAMKTLG C556_AGRTB 85 85
DAETALAQLPADQAGVGNTLKTLG C556_AGRTA 87 87
AVAALEPAAGAGQKELAAAVGKVG CYCP_RHOSH 93 93
KAVDGAKGKIKDVDTLKAAMQPIG C556_RHOPA 91 91
AAATAAQGTIKDEASLKANIGGVL CYCP_RHOPA 87 87
ATLAQMVDDGEEFSALRRQVGAVG CYCP_PARSP 96 96
CYTCHROMECII2 Length of motif = 12 Motif number = 2
Class II cytochrome c motif II - 1
PCODE ST INT
GQTCKACHDDFR CYCP_RHOTE 119 -1
GGTCKACHDDYR CYCP_RHOCA 115 -1
GGTCKACHKEFK CYCP_RHORU 113 -1
GASCKACHDAYR CYCP_ALCSP 113 -1
GGTCKGCHETFR CYCP_RHOPH 113 -1
GAACKSCHEKYR CYCP_CHRVI 118 -1
GGACKGCHDKFK CYCP_RHOGE 116 -1
GGTCKACHDDYR CYCP_RHOSP 114 -1
GKVCKACHEEFK CYCP_RHOFU 115 -1
GKVCKACHEEFK CYCP_RHOMO 115 -1
GADCGACHQTYR C556_AGRTC 108 -1
GADCGTCHQTYR C556_AGRTB 108 -1
GGNCGACHQAYR C556_AGRTA 110 -1
GTGCKSCHDDFR CYCP_RHOSH 116 -1
GKACGNCHENFR C556_RHOPA 114 -1
LGNCKSCHDDFR CYCP_RHOPA 110 -1
GKSCKGCHDDFR CYCP_PARSP 119 -1
FINAL MOTIF SETS
CYTCHROMECII1 Length of motif = 24 Motif number = 1
Class II cytochrome c motif I - 2
PCODE ST INT
GAEVIAAANAGDATAFGAALQKLG CYCP_RHOCA 92 92
ANELAKVAATGDAAAVKAQFGKVG CYCP_RHOTE 96 96
GMELIAAANTGEASAFGPALKKLG CYCP_RHOSP 91 91
AKALAQAATAGDTAQMGKALAALG CYCP_RHOPH 90 90
ALELASAAETGDKAAIGAKLQALG CYCP_RHORU 90 90
IVKLSAAADAGDLDKLRAAFGDVG CYCP_ALCSP 90 90
ANTLAEVAATGEAEAVKTAFGDVG CYCP_CHRVI 118 118
DADKVLASLPADQAGVTAAMQTLG C556_AGRTC 85 85
AAAKMQAAAGTDLASLQGAMRDLG C554_RHOSH 116 116
VDKLDAAGKTGDFAQIKAAVGETG CYCP_RHOGE 93 93
ESTKLAAAAKAGPDALKAQAAATG CYCP_RHOFU 92 92
ESTKLAAAAKAGPDALKAQAAATG CYCP_RHOMO 92 92
DAETALAQLPADQAGVGNTLKTLG C556_AGRTA 87 87
AVAALEPAAGAGQKELAAAVGKVG CYCP_RHOSH 93 93
DADIVLANLPGDQAGVATAMKTLG C556_AGRTB 85 85
AAATAAQGTIKDEASLKANIGGVL CYCP_RHOPA 87 87
KAVDGAKGKIKDVDTLKAAMQPIG C556_RHOPA 91 91
CYTCHROMECII2 Length of motif = 12 Motif number = 2
Class II cytochrome c motif II - 2
PCODE ST INT
GGTCKACHDDYR CYCP_RHOCA 115 -1
GQTCKACHDDFR CYCP_RHOTE 119 -1
GGTCKACHDDYR CYCP_RHOSP 114 -1
GGTCKGCHETFR CYCP_RHOPH 113 -1
GGTCKACHKEFK CYCP_RHORU 113 -1
GASCKACHDAYR CYCP_ALCSP 113 -1
GAACKSCHEKYR CYCP_CHRVI 141 -1
GADCGACHQTYR C556_AGRTC 108 -1
GAACGSCHETYR C554_RHOSH 139 -1
GGACKGCHDKFK CYCP_RHOGE 116 -1
GKVCKACHEEFK CYCP_RHOFU 115 -1
GKVCKACHEEFK CYCP_RHOMO 115 -1
GGNCGACHQAYR C556_AGRTA 110 -1
GTGCKSCHDDFR CYCP_RHOSH 116 -1
GADCGTCHQTYR C556_AGRTB 108 -1
LGNCKSCHDDFR CYCP_RHOPA 110 -1
GKACGNCHENFR C556_RHOPA 114 -1
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