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PR00606

Identifier
CYTCHROMECID  [View Relations]  [View Alignment]  
Accession
PR00606
No. of Motifs
5
Creation Date
18-JUL-1996  (UPDATE 07-JUN-1999)
Title
Class ID cytochrome C signature
Database References

PROSITE; PS00190 CYTOCHROME_C
BLOCKS; BL00190
INTERPRO; IPR002324
PDB; 1COR; 1CCH; 351C
SCOP; 1COR; 1CCH; 351C
CATH; 1COR; 1CCH; 351C
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. ALMASSY, R.J. AND DICKERSON, R.E.
Pseudomonas cytochrome c551 at 2.0 A resolution: enlargement of the 
cytochrome c family.
PROC.NATL.ACAD.SCI.U.S.A. 75 2674-2678 (1978).
 
4. CAI, M., BRADFORD, E.G. AND TIMKOVICH, R.
Investigation of the solution conformation of cytochrome c-551 from 
Pseudomonas stutzeri.
BIOCHEMISTRY 31 8603-8612 (1992).

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 ID (cyt c8) includes such bacterial proteins as 
Pseudomonas spp. cyt c-551, Hydrogenobacter thermophilus cyt c-552 and 
Rhodospirillum tenue cyt c-553 [2]. Sequence characteristics include several
Pro residues around the sixth ligand Met, and a conserved Trp residue near
the C-terminus.
   
The 3D structures of cyt c-551 from Pseudomonas aeruginosa and Pseudomonas
stutzeri have been determined [3]. The proteins consist of 5 alpha-helices;
three "core" helices form a "basket" around the haem group, with one haem 
edge exposed to the solvent. 
 
CYTCHROMECID is a 5-element fingerprint that provides a signature for class 
ID cyt c. The fingerprint was derived from an initial alignment of 9
sequences: motifs 1 and 2 are adjacent, motif 1 including helix 2, two
invariant Cys residues of which covalently bind the haem group, and a His
residue providing the fifth haem iron ligand (cf. PROSITE pattern
CYTOCHROME_C); motif 4 spans a Pro-rich region between helices 4 and 5, and
includes an invariant Met, which provides the sixth haem iron ligand; and
motifs 3 and 5 contain conserved Trp residues. Two iterations on OWL28.0
were required to reach convergence, at which point a true set comprising 11
sequences was identified. A single partial match was also found, a Pseudo-
monas hydrogenothermophila cyt c-552 fragment that lacks motifs 4 and 5. 
 
An update on SPTR37_9f identified a true set of 11 sequences.
Summary Information
11 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
51111111111
400000
300000
200000
12345
True Positives
C551_AZOVI    C551_CHRVI    C551_PSEAE    C551_PSEDE    
C551_PSEFC C551_PSEME C551_PSEST C552_HYDTH
C552_NITEU CY2_RHOGE CY2_RHOTE
Sequence Titles
C551_AZOVI  CYTOCHROME C-551 (C551) - AZOTOBACTER VINELANDII. 
C551_CHRVI CYTOCHROME C-551 (C551) - CHROMATIUM VINOSUM.
C551_PSEAE CYTOCHROME C-551 PRECURSOR (C551) (CYTOCHROME C8) - PSEUDOMONAS AERUGINOSA.
C551_PSEDE CYTOCHROME C-551 (C551) (CYTOCHROME C8) - PSEUDOMONAS DENITRIFICANS.
C551_PSEFC CYTOCHROME C-551 (C551) (CYTOCHROME C8) - PSEUDOMONAS FLUORESCENS BIOTYPE C.
C551_PSEME CYTOCHROME C-551 (C551) (CYTOCHROME C8) - PSEUDOMONAS MENDOCINA.
C551_PSEST CYTOCHROME C-551 PRECURSOR (C551) (CYTOCHROME C8) - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
C552_HYDTH CYTOCHROME C-552 PRECURSOR (C552) - HYDROGENOBACTER THERMOPHILUS.
C552_NITEU CYTOCHROME C-552 PRECURSOR (C552) (C-551) - NITROSOMONAS EUROPAEA.
CY2_RHOGE CYTOCHROME C2 - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GELATINOSA).
CY2_RHOTE CYTOCHROME C2 - RHODOCYCLUS TENUIS (RHODOSPIRILLUM TENUE).
Scan History
OWL28_0    2  100  NSINGLE    
SPTR37_9f 2 35 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
LFKAKACVACHSVD C551_PSEDE 6 6 -
LAQTKGCLACHNPE CY2_RHOTE 6 6 -
LAQKSGCTVCHSVE C551_CHRVI 4 4 -
LATKAGCAVCHQPT CY2_RHOGE 6 6 -
LFKSKPCAACHSVD C550_PSEST 28 28 -
LFKSKPCGACHSVQ C551_PSEME 6 6 -
LFKNKGCVACHAID C551_PSEAE 28 28 -
LFKSKPCAACHTID C551_PSEFC 6 6 -
LAKQKGCMACHDLK C552_HYDTH 22 22 -

Motif 2 width=14
Element Seqn Id St Int Rpt
KLVGPAFHDVAAKY C551_PSEDE 21 1 -
AIVGPAYKDVAAKY C551_CHRVI 19 1 -
KMVGPALKEVAAKN C550_PSEST 43 1 -
KGLGPSYQEIAKKY CY2_RHOGE 21 1 -
KLVGPALKDVAAKN C551_PSEME 21 1 -
KMVGPAYKDVAAKF C551_PSEAE 43 1 -
KMVGPALKEVAAKN C551_PSEFC 21 1 -
KKVGPAYADVAKKY C552_HYDTH 37 1 -
KVVGPAYGWVAKKY CY2_RHOTE 21 1 -

Motif 3 width=14
Element Seqn Id St Int Rpt
LVAKVMAGGVGNWG C551_CHRVI 42 9 -
LALHIKNGSQGVWG C550_PSEST 66 9 -
LAGHIKNGSTGVWG C551_PSEME 44 9 -
LAQRIKNGSQGVWG C551_PSEAE 66 9 -
LAGHIKNGTQGNWG C551_PSEFC 44 9 -
LAGKIKKGGSGVWG C552_HYDTH 60 9 -
ITNSIKTGSKGNWG C551_PSEDE 44 9 -
LVAKVMAGGQGVWA CY2_RHOTE 44 9 -
MAERVRKGSVGIFG CY2_RHOGE 44 9 -

Motif 4 width=11
Element Seqn Id St Int Rpt
IPMPPNPVTEE C550_PSEST 81 1 -
MPMPPNPVTEE C551_PSEME 59 1 -
IPMPPNAVSDD C551_PSEAE 81 1 -
IPMPPNQVTDA C551_PSEFC 59 1 -
VPMPPQNVTDA C552_HYDTH 75 1 -
IPMPPNAVSPE C551_PSEDE 59 1 -
IPMPANNVTKE CY2_RHOTE 64 6 -
VPMPPNAHVPA C551_CHRVI 57 1 -
LPMTPTPPARI CY2_RHOGE 59 1 -

Motif 5 width=11
Element Seqn Id St Int Rpt
DIKALVTWILG C551_CHRVI 69 1 -
DLKLVIDWILK CY2_RHOGE 73 3 -
EAKTLAEWVLT C551_PSEME 70 0 -
EAKILAEWVLS C550_PSEST 92 0 -
EAQTLAKWVLS C551_PSEAE 92 0 -
EALTLAQWVLS C551_PSEFC 70 0 -
EAKQLAQWILS C552_HYDTH 86 0 -
EAKTLAEWIVT C551_PSEDE 70 0 -
EATRLVKWVLS CY2_RHOTE 75 0 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
LFKSKPCAACHSVD C551_PSEST 28 28 -
LFKSKPCGACHSVQ C551_PSEME 6 6 -
LFKNKGCVACHAID C551_PSEAE 28 28 -
LFKSKPCAACHTID C551_PSEFC 6 6 -
LYKTKGCTVCHAID C551_AZOVI 6 6 -
LAKQKGCMACHDLK C552_HYDTH 22 22 -
LFKAKACVACHSVD C551_PSEDE 6 6 -
LAKKNNCIACHQVE C552_NITEU 26 26 -
LAQTKGCLACHNPE CY2_RHOTE 6 6 -
LAQKSGCTVCHSVE C551_CHRVI 4 4 -
LATKAGCAVCHQPT CY2_RHOGE 6 6 -

Motif 2 width=14
Element Seqn Id St Int Rpt
KMVGPALKEVAAKN C551_PSEST 43 1 -
KLVGPALKDVAAKN C551_PSEME 21 1 -
KMVGPAYKDVAAKF C551_PSEAE 43 1 -
KMVGPALKEVAAKN C551_PSEFC 21 1 -
KLVGPSFKEVTAKY C551_AZOVI 21 1 -
KKVGPAYADVAKKY C552_HYDTH 37 1 -
KLVGPAFHDVAAKY C551_PSEDE 21 1 -
KVVGPALKDIAAKY C552_NITEU 41 1 -
KVVGPAYGWVAKKY CY2_RHOTE 21 1 -
AIVGPAYKDVAAKY C551_CHRVI 19 1 -
KGLGPSYQEIAKKY CY2_RHOGE 21 1 -

Motif 3 width=14
Element Seqn Id St Int Rpt
LALHIKNGSQGVWG C551_PSEST 66 9 -
LAGHIKNGSTGVWG C551_PSEME 44 9 -
LAQRIKNGSQGVWG C551_PSEAE 66 9 -
LAGHIKNGTQGNWG C551_PSEFC 44 9 -
LAAKIKAGGSGNWG C551_AZOVI 44 9 -
LAGKIKKGGSGVWG C552_HYDTH 60 9 -
ITNSIKTGSKGNWG C551_PSEDE 44 9 -
LAGKIKGGSSGVWG C552_NITEU 64 9 -
LVAKVMAGGQGVWA CY2_RHOTE 44 9 -
LVAKVMAGGVGNWG C551_CHRVI 42 9 -
MAERVRKGSVGIFG CY2_RHOGE 44 9 -

Motif 4 width=11
Element Seqn Id St Int Rpt
IPMPPNPVTEE C551_PSEST 81 1 -
MPMPPNPVTEE C551_PSEME 59 1 -
IPMPPNAVSDD C551_PSEAE 81 1 -
IPMPPNQVTDA C551_PSEFC 59 1 -
IPMPPNPVSEA C551_AZOVI 59 1 -
VPMPPQNVTDA C552_HYDTH 75 1 -
IPMPPNAVSPE C551_PSEDE 59 1 -
IPMPPNVNVSD C552_NITEU 79 1 -
IPMPANNVTKE CY2_RHOTE 64 6 -
VPMPPNAHVPA C551_CHRVI 57 1 -
LPMTPTPPARI CY2_RHOGE 59 1 -

Motif 5 width=11
Element Seqn Id St Int Rpt
EAKILAEWVLS C551_PSEST 92 0 -
EAKTLAEWVLT C551_PSEME 70 0 -
EAQTLAKWVLS C551_PSEAE 92 0 -
EALTLAQWVLS C551_PSEFC 70 0 -
EAKTLAEWVLT C551_AZOVI 70 0 -
EAKQLAQWILS C552_HYDTH 86 0 -
EAKTLAEWIVT C551_PSEDE 70 0 -
DAKALADWILT C552_NITEU 91 1 -
EATRLVKWVLS CY2_RHOTE 75 0 -
DIKALVTWILG C551_CHRVI 69 1 -
DLKLVIDWILK CY2_RHOGE 73 3 -