WORKLIST ENTRIES (1):
CYTCHROMECIE View alignment View Structure Class IE cytochrome C signature
Type of fingerprint: COMPOUND with 4 elements
Links:
PRINTS; PR00603 CYTOCHROMEC1; PR00604 CYTCHRMECIAB; PR00605 CYTCHROMECIC
PRINTS; PR00606 CYTCHROMECID; PR00608 CYTCHROMECII; PR00609 CYTOCHROMEC3
PRINTS; PR00610 CYTOCHROMEF
INTERPRO; IPR002323
PROSITE; PS00190 CYTOCHROME_C
PDB; 1CC5 3Dinfo
SCOP; 1CC5
CATH; 1CC5
Creation date 19-JUL-1996; UPDATE 26-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. CARTER, D.C., MELIS, K.A., O'DONNELL, S.E., BURGESS, B.K., FUREY, W.F.,
WANG, B.-C. AND STOUT, C.D.
Crystal structure of Azotobacter cytochrome c5 at 2.5A resolution.
J.MOL.BIOL. 184 279-295 (1985).
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 IE includes such bacterial proteins as cyt c5,
cyt c-555 and Ectothiorhodospira spp. cyt c-551. The 3D structure of cyt c5
from Azotobacter vinelandii has been determined [3]. The protein consists
of 5 alpha-helices; three "core" helices form a "basket" around the haem
group, with one haem edge exposed to the solvent.
CYTCHROMECIE is a 4-element fingerprint that provides a signature for class
IE cyt c. The fingerprint was derived from an initial alignment of 6
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 2 includes an invariant Trp residue; motif 3 lies
between helices 4 and 5, and includes an invariant Met, which provides the
sixth haem iron ligand. A single iteration on OWL28.0 was required to reach
convergence, no further sequences being identified beyond the starting set.
Eight partial matches were also found, all of which are class IC cyt c (cyt
c6) that match motifs 1 and 3.
An update on SPTR37_9f identified a true set of 8 sequences.
SUMMARY INFORMATION
8 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
4| 8 8 8 8
3| 0 0 0 0
2| 0 0 0 0
--+---------------------
| 1 2 3 4
True positives..
O31274 CYC5_AZOVI CYC5_PSEME C551_ECTHL
O52685 C555_CHLLT C551_ECTHA C555_PROAE
PROTEIN TITLES
O31274 CYTOCHROME C5 - AZOTOBACTER VINELANDII.
CYC5_AZOVI CYTOCHROME C5 - AZOTOBACTER VINELANDII.
CYC5_PSEME CYTOCHROME C5 - PSEUDOMONAS MENDOCINA.
C551_ECTHL CYTOCHROME C-551 (C551) - ECTOTHIORHODOSPIRA HALOCHLORIS.
O52685 MONO-HEME C-TYPE CYTOCHROME SCYA - SHEWANELLA PUTREFACIENS.
C555_CHLLT CYTOCHROME C-555 (C555) - CHLOROBIUM LIMICOLA F.SP. THIOSULF
C551_ECTHA CYTOCHROME C-551 (C551) - ECTOTHIORHODOSPIRA HALOPHILA.
C555_PROAE CYTOCHROME C-555 (C555) - PROSTHECOCHLORIS AESTUARII.
SCAN HISTORY
OWL28_0 1 50 NSINGLE
SPTR37_9f 2 11 NSINGLE
INITIAL MOTIF SETS
CYTCHROMECIE1 Length of motif = 12 Motif number = 1
Class IE cytochrome c motif I - 1
PCODE ST INT
TCSSCHDRGVAG C551_ECTHA 13 13
TCASCHDRGTAG C551_ECTHL 13 13
SCAMCHKTGMMG C555_CHLLT 13 13
NCASCHAAGIMG C555_PROAE 22 22
YCNACHGTGLLN CYC5_AZOVI 14 14
HCNACHGAGVLG CYC5_PSEME 18 18
CYTCHROMECIE2 Length of motif = 11 Motif number = 2
Class IE cytochrome c motif II - 1
PCODE ST INT
GAPELNAPEDW C551_ECTHA 24 -1
GAPKINEPGDW C551_ECTHL 24 -1
GAPKVGDKAAW C555_CHLLT 24 -1
GAPKTGTARKW C555_PROAE 33 -1
NAPKVGDSAAW CYC5_AZOVI 25 -1
GAPKIGDTAAW CYC5_PSEME 29 -1
CYTCHROMECIE3 Length of motif = 13 Motif number = 3
Class IE cytochrome c motif III - 1
PCODE ST INT
GKGAMPAYDGRAD C551_ECTHA 51 16
GKGAMPAYDGRAD C551_ECTHL 51 16
TKGMMPAKGGNPK C555_CHLLT 56 21
SKTFMPAKGGNPD C555_PROAE 69 25
GLNAMPPKGTCAD CYC5_AZOVI 55 19
GINAMPPKGTCAD CYC5_PSEME 59 19
CYTCHROMECIE4 Length of motif = 12 Motif number = 4
Class IE cytochrome c motif IV - 1
PCODE ST INT
REDLVKAIEYML C551_ECTHA 64 0
RDEVKEAVEYML C551_ECTHL 64 0
DAQVGNAVAYMV C555_CHLLT 71 2
DKQVGDAVAYMV C555_PROAE 84 2
DDELKAAIGKMS CYC5_AZOVI 70 2
DDELREAIQKMS CYC5_PSEME 74 2
FINAL MOTIF SETS
CYTCHROMECIE1 Length of motif = 12 Motif number = 1
Class IE cytochrome c motif I - 2
PCODE ST INT
YCNACHGTGLLN CYC5_AZOVI 14 14
YCNACHGTGLLN O31274 65 65
HCNACHGAGVLG CYC5_PSEME 18 18
TCASCHDRGTAG C551_ECTHL 13 13
ACTVCHSMGVAG O52685 31 31
SCAMCHKTGMMG C555_CHLLT 13 13
TCSSCHDRGVAG C551_ECTHA 13 13
NCASCHAAGIMG C555_PROAE 22 22
CYTCHROMECIE2 Length of motif = 11 Motif number = 2
Class IE cytochrome c motif II - 2
PCODE ST INT
NAPKVGDSAAW CYC5_AZOVI 25 -1
NAPKVGDSAAW O31274 76 -1
GAPKIGDTAAW CYC5_PSEME 29 -1
GAPKINEPGDW C551_ECTHL 24 -1
GAPKSHNTADW O52685 42 -1
GAPKVGDKAAW C555_CHLLT 24 -1
GAPELNAPEDW C551_ECTHA 24 -1
GAPKTGTARKW C555_PROAE 33 -1
CYTCHROMECIE3 Length of motif = 13 Motif number = 3
Class IE cytochrome c motif III - 2
PCODE ST INT
GLNAMPPKGTCAD CYC5_AZOVI 55 19
GLNAMPPKGTCAD O31274 106 19
GINAMPPKGTCAD CYC5_PSEME 59 19
GKGAMPAYDGRAD C551_ECTHL 51 16
GLNAMPPGGMCTD O52685 70 17
TKGMMPAKGGNPK C555_CHLLT 56 21
GKGAMPAYDGRAD C551_ECTHA 51 16
SKTFMPAKGGNPD C555_PROAE 69 25
CYTCHROMECIE4 Length of motif = 12 Motif number = 4
Class IE cytochrome c motif IV - 2
PCODE ST INT
DDELKAAIGKMS CYC5_AZOVI 70 2
DDELKAAIGKMS O31274 121 2
DDELREAIQKMS CYC5_PSEME 74 2
RDEVKEAVEYML C551_ECTHL 64 0
DEDYKAAIEFMS O52685 85 2
DAQVGNAVAYMV C555_CHLLT 71 2
REDLVKAIEYML C551_ECTHA 64 0
DKQVGDAVAYMV C555_PROAE 84 2
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