WORKLIST ENTRIES (1):
CYTCHROMECID View alignment View Structure Class ID cytochrome C signature
Type of fingerprint: COMPOUND with 5 elements
Links:
PRINTS; PR00603 CYTOCHROMEC1; PR00604 CYTCHRMECIAB; PR00605 CYTCHROMECIC
PRINTS; PR00607 CYTCHROMECIE; PR00608 CYTCHROMECII; PR00609 CYTOCHROMEC3
PRINTS; PR00610 CYTOCHROMEF
INTERPRO; IPR002324
PROSITE; PS00190 CYTOCHROME_C
PDB; 1COR 3Dinfo; 1CCH 3Dinfo; 351C 3Dinfo
SCOP; 1COR; 1CCH; 351C
CATH; 1COR; 1CCH; 351C
Creation date 18-JUL-1996; UPDATE 07-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. ALMASSY, R.J. AND DICKERSON, R.E.
Pseudomonas cytochrome c551 at 2.0A 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).
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 FINGERPRINT INDEX
5| 11 11 11 11 11
4| 0 0 0 0 0
3| 0 0 0 0 0
2| 0 0 0 0 0
--+--------------------------
| 1 2 3 4 5
True positives..
C551_PSEST C551_PSEME C551_PSEAE C551_PSEFC
C551_AZOVI C552_HYDTH C551_PSEDE C552_NITEU
CY2_RHOTE C551_CHRVI CY2_RHOGE
PROTEIN TITLES
C551_PSEST CYTOCHROME C-551 PRECURSOR (C551) (CYTOCHROME C8) - PSEUDOMO
C551_PSEME CYTOCHROME C-551 (C551) (CYTOCHROME C8) - PSEUDOMONAS MENDOC
C551_PSEAE CYTOCHROME C-551 PRECURSOR (C551) (CYTOCHROME C8) - PSEUDOMO
C551_PSEFC CYTOCHROME C-551 (C551) (CYTOCHROME C8) - PSEUDOMONAS FLUORE
C551_AZOVI CYTOCHROME C-551 (C551) - AZOTOBACTER VINELANDII.
C552_HYDTH CYTOCHROME C-552 PRECURSOR (C552) - HYDROGENOBACTER THERMOPH
C551_PSEDE CYTOCHROME C-551 (C551) (CYTOCHROME C8) - PSEUDOMONAS DENITR
C552_NITEU CYTOCHROME C-552 PRECURSOR (C552) (C-551) - NITROSOMONAS EUR
CY2_RHOTE CYTOCHROME C2 - RHODOCYCLUS TENUIS (RHODOSPIRILLUM TENUE).
C551_CHRVI CYTOCHROME C-551 (C551) - CHROMATIUM VINOSUM.
CY2_RHOGE CYTOCHROME C2 - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GE
SCAN HISTORY
OWL28_0 2 100 NSINGLE
SPTR37_9f 2 35 NSINGLE
INITIAL MOTIF SETS
CYTCHROMECID1 Length of motif = 14 Motif number = 1
Class ID cytochrome c motif I - 1
PCODE ST INT
LFKSKPCAACHSVD C550_PSEST 28 28
LFKSKPCAACHTID C551_PSEFC 6 6
LFKNKGCVACHAID C551_PSEAE 28 28
LFKAKACVACHSVD C551_PSEDE 6 6
LFKSKPCGACHSVQ C551_PSEME 6 6
LAQKSGCTVCHSVE C551_CHRVI 4 4
LAKQKGCMACHDLK C552_HYDTH 22 22
LAQTKGCLACHNPE CY2_RHOTE 6 6
LATKAGCAVCHQPT CY2_RHOGE 6 6
CYTCHROMECID2 Length of motif = 14 Motif number = 2
Class ID cytochrome c motif II - 1
PCODE ST INT
KMVGPALKEVAAKN C550_PSEST 43 1
KMVGPALKEVAAKN C551_PSEFC 21 1
KMVGPAYKDVAAKF C551_PSEAE 43 1
KLVGPAFHDVAAKY C551_PSEDE 21 1
KLVGPALKDVAAKN C551_PSEME 21 1
AIVGPAYKDVAAKY C551_CHRVI 19 1
KKVGPAYADVAKKY C552_HYDTH 37 1
KVVGPAYGWVAKKY CY2_RHOTE 21 1
KGLGPSYQEIAKKY CY2_RHOGE 21 1
CYTCHROMECID3 Length of motif = 14 Motif number = 3
Class ID cytochrome c motif III - 1
PCODE ST INT
LALHIKNGSQGVWG C550_PSEST 66 9
LAGHIKNGTQGNWG C551_PSEFC 44 9
LAQRIKNGSQGVWG C551_PSEAE 66 9
ITNSIKTGSKGNWG C551_PSEDE 44 9
LAGHIKNGSTGVWG C551_PSEME 44 9
LVAKVMAGGVGNWG C551_CHRVI 42 9
LAGKIKKGGSGVWG C552_HYDTH 60 9
LVAKVMAGGQGVWA CY2_RHOTE 44 9
MAERVRKGSVGIFG CY2_RHOGE 44 9
CYTCHROMECID4 Length of motif = 11 Motif number = 4
Class ID cytochrome c motif IV - 1
PCODE ST INT
IPMPPNPVTEE C550_PSEST 81 1
IPMPPNQVTDA C551_PSEFC 59 1
IPMPPNAVSDD C551_PSEAE 81 1
IPMPPNAVSPE C551_PSEDE 59 1
MPMPPNPVTEE C551_PSEME 59 1
VPMPPNAHVPA C551_CHRVI 57 1
VPMPPQNVTDA C552_HYDTH 75 1
IPMPANNVTKE CY2_RHOTE 64 6
LPMTPTPPARI CY2_RHOGE 59 1
CYTCHROMECID5 Length of motif = 11 Motif number = 5
Class ID cytochrome c motif V - 1
PCODE ST INT
EAKILAEWVLS C550_PSEST 92 0
EALTLAQWVLS C551_PSEFC 70 0
EAQTLAKWVLS C551_PSEAE 92 0
EAKTLAEWIVT C551_PSEDE 70 0
EAKTLAEWVLT C551_PSEME 70 0
DIKALVTWILG C551_CHRVI 69 1
EAKQLAQWILS C552_HYDTH 86 0
EATRLVKWVLS CY2_RHOTE 75 0
DLKLVIDWILK CY2_RHOGE 73 3
FINAL MOTIF SETS
CYTCHROMECID1 Length of motif = 14 Motif number = 1
Class ID cytochrome c motif I - 2
PCODE ST INT
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
CYTCHROMECID2 Length of motif = 14 Motif number = 2
Class ID cytochrome c motif II - 2
PCODE ST INT
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
CYTCHROMECID3 Length of motif = 14 Motif number = 3
Class ID cytochrome c motif III - 2
PCODE ST INT
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
CYTCHROMECID4 Length of motif = 11 Motif number = 4
Class ID cytochrome c motif IV - 2
PCODE ST INT
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
CYTCHROMECID5 Length of motif = 11 Motif number = 5
Class ID cytochrome c motif V - 2
PCODE ST INT
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
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