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PR00609

Identifier
CYTOCHROMEC3  [View Relations]  [View Alignment]  
Accession
PR00609
No. of Motifs
4
Creation Date
03-JUL-1996  (UPDATE 07-JUN-1999)
Title
Class III cytochrome C signature
Database References

PROSITE; PS00190 CYTOCHROME_C
BLOCKS; BL00190
INTERPRO; IPR002322
PDB; 1CTH; 2CDV; 2CY3; 2CYM
SCOP; 1CTH; 2CDV; 2CY3; 2CYM
CATH; 1CTH; 2CDV; 2CY3; 2CYM
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. COUTINHO, I.B. AND XAVIER, A.V.
Tetraheme cytochromes. 
METHODS ENZYMOL. 243 119-140 (1994). 

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 III comprises the low 
redox potential multiple haem cytochromes: cyt c7 (trihaem), c3 (tetrahaem),
and high-molecular-weight cyt c, 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 [3]. 
 
The 3D structures of a number of cyt c3 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 [3]. 
 
CYTOCHROMEC3 is a 4-element fingerprint that provides a signature for the
class III cyt c. The fingerprint was derived from an initial alignment of 9
sequences: motifs 1 and 2 are adjacent, motif 1 including an invariant Phe
and two invariant His residues, which function as the axial ligands for two
different haems (in tetrahaem cyt c, these are haem 1 and 3; in trihaem cyt
c, they are haem 1 and haem 2); motifs 2-4 each include 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). In
tetrahaem cyt c, motifs 2-4 bind haem groups 1, 3 and 4 res.; in trihaem cyt
c, they bind haem groups 1, 2 and 3 res.. In tetrahaem cyt c and HMC, motif
2 includes two adjacent His residues: in tetrahaem cyt c these provide the
axial ligands to haem groups 1 and 2 [3]; in trihaem cyt c the second His
is replaced by Glu. Two iterations on OWL28.0 were required to reach
convergence, at which point a true set comprising 12 sequences was identified.
 
An update on SPTR37_9f identified a true set of 10 sequences.
Summary Information
10 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
410101010
30000
20000
1234
True Positives
CY31_DESDN    CY32_DESDN    CYC3_DESAC    CYC3_DESDE    
CYC3_DESGI CYC3_DESSA CYC3_DESVH CYC3_DESVM
HMWC_DESVH P94691
Sequence Titles
CY31_DESDN  CYTOCHROME C3, 13 KD - DESULFOVIBRIO DESULFURICANS (STRAIN NORWAY 4). 
CY32_DESDN CYTOCHROME C3, 26 KD - DESULFOVIBRIO DESULFURICANS (STRAIN NORWAY 4).
CYC3_DESAC CYTOCHROME C3 (CYTOCHROME C7) (C551.5) - DESULFUROMONAS ACETOXIDANS (CHLOROPSEUDOMONAS ETHYLICA).
CYC3_DESDE CYTOCHROME C3 - DESULFOVIBRIO DESULFURICANS.
CYC3_DESGI CYTOCHROME C3 - DESULFOVIBRIO GIGAS.
CYC3_DESSA CYTOCHROME C3 - DESULFOVIBRIO SALEXIGENS.
CYC3_DESVH CYTOCHROME C3 PRECURSOR - DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH).
CYC3_DESVM CYTOCHROME C3 PRECURSOR - DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI).
HMWC_DESVH HIGH-MOLECULAR-WEIGHT CYTOCHROME C PRECURSOR (CYTOCHROME CC3) - DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH).
P94691 BASIC PRE-CYTOCHROME C3 PRECURSOR - DESULFOVIBRIO AFRICANUS.
Scan History
OWL28_0    2  75   NSINGLE    
SPTR37_9f 2 19 NSINGLE
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
PVAFSHKGHA CYC3_DESDE 21 21 -
PVDFSHKGHA CYC3_DESSA 21 21 -
PVVFNHSTHK CYC3_DESVM 17 17 -
PVVFNHSTHK CYC3_DESVH 39 39 -
PVAFDHKAHE HMWC_DESVH 293 293 -
DVTFNHASHM CY32_DESDN 25 25 -
LVVFNHSTHK CYC3_DESGI 20 20 -
TVPFPHTKHA CY31_DESDN 31 31 -
NVTFDHKAHA CYC3_DESAC 12 12 -

Motif 2 width=8
Element Seqn Id St Int Rpt
MDCKTCHH CYC3_DESDE 32 1 -
LDCTKCHH CYC3_DESSA 32 1 -
VKCGDCHH CYC3_DESVM 28 1 -
VKCGDCHH CYC3_DESVH 50 1 -
NDCRTCHH HMWC_DESVH 306 3 -
IACQQCHH CY32_DESDN 36 1 -
VKCBBCHH CYC3_DESGI 31 1 -
VECVQCHH CY31_DESDN 42 1 -
LGCDACHE CYC3_DESAC 24 2 -

Motif 3 width=12
Element Seqn Id St Int Rpt
KSCVGCHKSMKK CYC3_DESDE 79 39 -
ISCVGCHKALKK CYC3_DESSA 80 40 -
KSCVGCHLETAG CYC3_DESVM 77 41 -
KSCVGCHVEVAG CYC3_DESVH 99 41 -
RSCVGCHNTRVQ HMWC_DESVH 347 33 -
KSCVGCHRELKR CY32_DESDN 84 40 -
PTCISCHKDKAG CYC3_DESGI 80 41 -
TQCIDCHALKKK CY31_DESDN 90 40 -
DACKTCHKSNNG CYC3_DESAC 47 15 -

Motif 4 width=8
Element Seqn Id St Int Rpt
PTKCTECH CYC3_DESDE 92 1 -
PTKCGDCH CYC3_DESSA 95 3 -
GCKGSKCH CYC3_DESVM 99 10 -
GCKKSKCH CYC3_DESVH 121 10 -
QPTCAGCH HMWC_DESVH 359 0 -
PLACNSCH CY32_DESDN 102 6 -
GCKGSACH CYC3_DESGI 102 10 -
PTACGKCH CY31_DESDN 108 6 -
PTKCGGCH CYC3_DESAC 59 0 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
PVAFSHKGHA CYC3_DESDE 21 21 -
PVDFSHKGHA CYC3_DESSA 21 21 -
PVVFNHSTHK CYC3_DESVM 17 17 -
PVVFNHSTHK CYC3_DESVH 39 39 -
KVKFSHKAHA P94691 46 46 -
PVAFDHKAHE HMWC_DESVH 293 293 -
DVTFNHASHM CY32_DESDN 25 25 -
LVVFNHSTHK CYC3_DESGI 20 20 -
TVPFPHTKHA CY31_DESDN 31 31 -
NVTFDHKAHA CYC3_DESAC 12 12 -

Motif 2 width=8
Element Seqn Id St Int Rpt
MDCKTCHH CYC3_DESDE 32 1 -
LDCTKCHH CYC3_DESSA 32 1 -
VKCGDCHH CYC3_DESVM 28 1 -
VKCGDCHH CYC3_DESVH 50 1 -
AACQKCHH P94691 62 6 -
NDCRTCHH HMWC_DESVH 306 3 -
IACQQCHH CY32_DESDN 36 1 -
VKCBBCHH CYC3_DESGI 31 1 -
VECVQCHH CY31_DESDN 42 1 -
LGCDACHE CYC3_DESAC 24 2 -

Motif 3 width=12
Element Seqn Id St Int Rpt
KSCVGCHKSMKK CYC3_DESDE 79 39 -
ISCVGCHKALKK CYC3_DESSA 80 40 -
KSCVGCHLETAG CYC3_DESVM 77 41 -
KSCVGCHVEVAG CYC3_DESVH 99 41 -
MSCQGCHKEMKT P94691 112 42 -
RSCVGCHNTRVQ HMWC_DESVH 347 33 -
KSCVGCHRELKR CY32_DESDN 84 40 -
PTCISCHKDKAG CYC3_DESGI 80 41 -
TQCIDCHALKKK CY31_DESDN 90 40 -
DACKTCHKSNNG CYC3_DESAC 47 15 -

Motif 4 width=8
Element Seqn Id St Int Rpt
PTKCTECH CYC3_DESDE 92 1 -
PTKCGDCH CYC3_DESSA 95 3 -
GCKGSKCH CYC3_DESVM 99 10 -
GCKKSKCH CYC3_DESVH 121 10 -
PTACAQCH P94691 130 6 -
QPTCAGCH HMWC_DESVH 359 0 -
PLACNSCH CY32_DESDN 102 6 -
GCKGSACH CYC3_DESGI 102 10 -
PTACGKCH CY31_DESDN 108 6 -
PTKCGGCH CYC3_DESAC 59 0 -