WORKLIST ENTRIES (1):
CYTCHROMECIC View alignment View Structure Class IC cytochrome C signature
Type of fingerprint: COMPOUND with 2 elements
Links:
PRINTS; PR00603 CYTOCHROMEC1; PR00604 CYTCHRMECIAB; PR00606 CYTCHROMECID
PRINTS; PR00607 CYTCHROMECIE; PR00608 CYTCHROMECII; PR00609 CYTOCHROMEC3
PRINTS; PR00610 CYTOCHROMEF
INTERPRO; IPR002329
PROSITE; PS00190 CYTOCHROME_C
PDB; 1C53 3Dinfo; 1CYI 3Dinfo
SCOP; 1C53; 1CYI
CATH; 1C53; 1CYI
Creation date 09-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. KERFELD, C.A., ANWAR, H.P., INTERRANTE, R., MERCHANT, S. AND YEATES, T.O.
The structure of chloroplast cytochrome c6 at 1.9A resolution: evidence
for functional oligomerization.
J.MOL.BIOL. 250 627-647 (1995).
4. NAKAGAWA, A., HIGUCHI, Y., YASUOKA, N., KATSUBE, Y. AND YAGI, T.
S-class cytochromes c have a variety of folding patterns: structure of
cytochrome c-553 from Desulfovibrio vulgaris determined by the
multi-wavelength anomalous dispersion method.
J.BIOCHEM. 108 701-703 (1990).
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 IC, "split-alpha-band" cyt c, possess a widened
or split alpha-band of lowered absorptivity. This class includes dihaem
cyt c4 and monohaem cyt c6 (cyt c-553) and cyt c-554.
The 3D structures of Chlamydomonas reinhardtii cyt c6 [3] and Desulfovibrio
vulgaris cyt c-553 [4] have been determined. The proteins consist of 4
alpha-helices; three "core" helices form a "basket" around the haem group,
with one haem edge exposed to the solvent.
CYTCHROMECIC is a 2-element fingerprint that provides a signature for the
class IC cyt c. The fingerprint was derived from an initial alignment of 17
sequences: motif 1 is situated in the loop between helices 1 and 2, and
includes two invariant Cys residues, which covalently bind the haem group,
and a His residue, which provides the fifth haem iron ligand (cf. PROSITE
pattern CYTOCHROME_C); and motif 2 includes both an invariant Met, which
provides the sixth haem iron ligand, and the N-terminal part of helix 4,
which contains a conserved aromatic residue. Two iterations on OWL28.0 were
required to reach convergence, at which point a true set comprising 41
sequences was identified.
An update on SPTR37_9f identified a true set of 50 sequences.
SUMMARY INFORMATION
50 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
2| 50 50
--+-----------
| 1 2
True positives..
CYC6_BUMFI CYC6_SYNSP CYC6_SYNEN CYC6_SYNLI
CYC6_PORPU CYC6_PORTE CYC6_SYNP2 CYC6_ANASP
CYC6_MONBR CYC6_SPIMA CYC6_ANASQ CYC6_MICAE
CYC6_PLEBO CYC6_PETFA CYC6_APHFL CYC6_SYNP7
CYC6_ANAVA CYC6_CHLRE CYC6_BRYMA CYC6_ALAES
CYC6_ANANI CYC6_SYNY3 CYC6_MONLU Q43945
Q51682 Q53114 Q03075 CYC6_EUGGR
CYC6_EUGVI Q05577 P72287 Q52689
O69780 CYC4_PSEST O30730 CYCA_GLUSU
O34215 CYC4_PSEAE C554_PARSP CYC4_AZOVI
CYCA_ACEPO Q46444 Q57536 C553_DESVM
C553_DESDN O34404 COX2_BACSU CYSD_CHLLT
C553_DESVH C554_THINE
PROTEIN TITLES
CYC6_BUMFI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BUM
CYC6_SYNSP CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYN
CYC6_SYNEN CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYN
CYC6_SYNLI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYN
CYC6_PORPU CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
CYC6_PORTE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - POR
CYC6_SYNP2 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
CYC6_ANASP CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
CYC6_MONBR CYTOCHROME C6 (CYTOCHROME C552) - MONORAPHIDIUM BRAUNII.
CYC6_SPIMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SPI
CYC6_ANASQ CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
CYC6_MICAE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - MIC
CYC6_PLEBO CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PLE
CYC6_PETFA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PET
CYC6_APHFL CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - APH
CYC6_SYNP7 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
CYC6_ANAVA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANA
CYC6_CHLRE CYTOCHROME C6 PRECURSOR (CYTOCHROME C552) - CHLAMYDOMONAS RE
CYC6_BRYMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BRY
CYC6_ALAES CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ALA
CYC6_ANANI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANA
CYC6_SYNY3 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
CYC6_MONLU CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PAV
Q43945 GENES FIXN, FIXO, FIXQ, FIXP AND FIXG - AZORHIZOBIUM CAULINO
Q51682 CCOP - PARACOCCUS DENITRIFICANS.
Q53114 CBB3-TYPE CYTOCHROME C OXIDASE CCOP SUBUNIT - RHODOBACTER SP
Q03075 CYTOCHROME C - BRADYRHIZOBIUM JAPONICUM.
CYC6_EUGGR CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUG
CYC6_EUGVI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUG
Q05577 FIXP PROTEIN - RHIZOBIUM MELILOTI.
P72287 FIXPC - RHIZOBIUM LEGUMINOSARUM.
Q52689 CCOP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O69780 DI-HEME CYTOCHROME C - RHIZOBIUM ETLI.
CYC4_PSEST CYTOCHROME C4 PRECURSOR - PSEUDOMONAS STUTZERI (PSEUDOMONAS
O30730 DI-HEME CYTOCHROME CP - RHODOBACTER CAPSULATUS (RHODOPSEUDOM
CYCA_GLUSU ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR (CYTOCH
O34215 CYTOCHROME C PRECURSOR - ERWINIA CYPRIPEDII.
CYC4_PSEAE CYTOCHROME C4 - PSEUDOMONAS AERUGINOSA.
C554_PARSP CYTOCHROME C-554(548) (C554) - PARACOCCUS SP. (STRAIN ATCC 1
CYC4_AZOVI CYTOCHROME C4 PRECURSOR - AZOTOBACTER VINELANDII.
CYCA_ACEPO ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR - ACETO
Q46444 QUINOHAEMOPROTEIN ETHANOL DEHYDROGENASE TYPE I PRECURSOR (EC
Q57536 CYTOCHROME C SUBUNIT OF ALCOHOL DEHYDROGENASE - ACETOBACTER
C553_DESVM CYTOCHROME C-553 PRECURSOR (C553) - DESULFOVIBRIO VULGARIS (
C553_DESDN CYTOCHROME C-553 (C553) - DESULFOVIBRIO DESULFURICANS (STRAI
O34404 CYTOCHROME C OXIDASE POLYPEPTIDE II (EC 1.9.3.1) - BACILLUS
COX2_BACSU CYTOCHROME C OXIDASE POLYPEPTIDE II PRECURSOR (EC 1.9.3.1) (
CYSD_CHLLT CYTOCHROME SUBUNIT OF SULFIDE DEHYDROGENASE (FC) (FCSD) (FLA
C553_DESVH CYTOCHROME C-553 PRECURSOR (C553) (LOW POTENTIAL CYTOCHROME
C554_THINE CYTOCHROME C-554(547) (C554) - THIOBACILLUS NEAPOLITANUS.
SCAN HISTORY
OWL28_0 2 160 NSINGLE
SPTR37_9f 2 100 NSINGLE
INITIAL MOTIF SETS
CYTCHROMECIC1 Length of motif = 12 Motif number = 1
Class IC cytochrome c motif I - 1
PCODE ST INT
KMCKSCHGADGS C553_DESDN 11 11
KSCVGCHGADGS C553_DESVM 8 8
AVCGACHGADGN CYC4_PSEAE 12 12
AVCGACHGPDGN CYC4_AZOVI 12 12
AVCGACHGVDGN PSU05988 32 32
GTCVACHGTDGQ C554_PARSP 12 12
ASCASCHGMQAQ C554_THINE 13 13
ANCAACHAGGNN CYC6_PORTE 12 12
ANCASCHAGGKN CYC6_ANASP 37 37
GNCAACHAGGAN CYC6_BRYMA 13 13
ANCASCHMGGKN CYC6_MICAE 8 8
ANCSACHAGGNN CYC6_ALAES 12 12
NNCSSCHVNGGN CYC6_EUGVI 8 8
GNCAACHMGGRN CYC6_CHLRE 70 70
ANCAACHASGGG CYC6_PLEBO 12 12
GNCAACHNGGLN CYC6_SYNY3 47 47
ANCAQCHVGGGN CYC6_APHFL 12 12
CYTCHROMECIC2 Length of motif = 23 Motif number = 2
Class IC cytochrome c motif II - 1
PCODE ST INT
KGMMERVVKSLTDEDIEVLATHI C553_DESDN 55 32
KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 54 34
VLEMTGLLTNLSNEDLADIAAYF CYC4_PSEAE 54 30
VLEMTGMLDNFSDQDLADLAAYF CYC4_AZOVI 63 39
VLEMTGMLDPLSDQDLEDIAAYF PSU05988 83 39
AALMTPMAQGLSDEDIADIAAYY C554_PARSP 57 33
SAIMAPNAAGLSEQDMDNLSAYI C554_THINE 65 40
KNAMPAFGGRLVDEDIEDAANYV CYC6_PORTE 55 31
KNAMPAFKGRLKPEQIEDVAAYV CYC6_ANASP 80 31
KGAMPAWSDRLDDEEIDGVVAYV CYC6_BRYMA 58 33
MGAMPAFGGRLSAEDIEAVANYV CYC6_MICAE 51 31
KNAMPAFGSRLAETDIEDVANFV CYC6_ALAES 55 31
KGPMPAWEGVLDESEIKEVTDYV CYC6_EUGVI 53 33
KGAMPAWADRLSEEEIQAVAEYV CYC6_CHLRE 115 33
KGAMPAFKGRLSDDQIQSVALYV CYC6_PLEBO 55 31
NGAMPGFKGRISDSDMEDVAAYV CYC6_SYNY3 90 31
KGAMPAFGIRLKAEQIENVAAYV CYC6_APHFL 55 31
FINAL MOTIF SETS
CYTCHROMECIC1 Length of motif = 12 Motif number = 1
Class IC cytochrome c motif I - 2
PCODE ST INT
ANCAACHAGGNN CYC6_BUMFI 12 12
ANCAACHMGGGN CYC6_SYNSP 12 12
GNCAACHMGGGN CYC6_SYNEN 12 12
GNCAACHMGGGN CYC6_SYNLI 12 12
ANCAACHAGGNN CYC6_PORPU 37 37
ANCAACHAGGNN CYC6_PORTE 12 12
ANCAACHAGGNN CYC6_SYNP2 36 36
ANCASCHAGGKN CYC6_ANASP 37 37
GNCAACHAGGGN CYC6_MONBR 13 13
ANCAACHMGGRN CYC6_SPIMA 12 12
ANCASCHAGGKN CYC6_ANASQ 37 37
ANCASCHMGGKN CYC6_MICAE 8 8
ANCAACHASGGG CYC6_PLEBO 12 12
ANCSACHAGGNN CYC6_PETFA 12 12
ANCAQCHVGGGN CYC6_APHFL 12 12
ANCAACHLGGRN CYC6_SYNP7 36 36
ANCASCHAGGKN CYC6_ANAVA 12 12
GNCAACHMGGRN CYC6_CHLRE 70 70
GNCAACHAGGAN CYC6_BRYMA 13 13
ANCSACHAGGNN CYC6_ALAES 12 12
ANCASCHLGGRN CYC6_ANANI 12 12
GNCAACHNGGLN CYC6_SYNY3 47 47
GNCAACHSVZZZ CYC6_MONLU 12 12
DNCAPCHGAGGG Q43945 125 125
TWCAQCHGSGAG Q51682 178 178
DNCAACHGEDGT Q53114 217 217
ENCVACHGDGGK Q03075 217 217
DNCSTCHVNGGN CYC6_EUGGR 8 8
NNCSSCHVNGGN CYC6_EUGVI 8 8
DNCASCHGADAK Q05577 216 216
DNCAACHGDDAK P72287 214 214
ENCASCHGEDAK Q52689 217 217
VNCAPCHGSGAS O69780 119 119
AVCGACHGVDGN CYC4_PSEST 32 32
TWCAQCHGAGAG O30730 119 119
HNCAICHMNDGT CYCA_GLUSU 338 338
DSCAACHKTDGS O34215 323 323
AVCGACHGADGN CYC4_PSEAE 12 12
GTCVACHGTDGQ C554_PARSP 12 12
AVCGACHGPDGN CYC4_AZOVI 32 32
KECAICHRNDGG CYCA_ACEPO 328 328
ANCVFCHGVPGV Q46444 633 633
EQCAICHRNDGG Q57536 329 329
KSCVGCHGADGS C553_DESVM 31 31
KMCKSCHGADGS C553_DESDN 11 11
KNCLSCHAVEPN O34404 269 269
KNCLSCHAVEPN COX2_BACSU 269 269
LSCAGCHGTDGK CYSD_CHLLT 16 16
KSCIGCHGADGS C553_DESVH 32 32
ASCASCHGMQAQ C554_THINE 13 13
CYTCHROMECIC2 Length of motif = 23 Motif number = 2
Class IC cytochrome c motif II - 2
PCODE ST INT
KNAMPAFGGRLSDSDIEDVANYV CYC6_BUMFI 55 31
KNAMPAFGGRLSEAQIENVAAYV CYC6_SYNSP 55 31
KNAMPAFAGRLTDEQIQDVAAYV CYC6_SYNEN 55 31
KNAMPAFAGRLTDEQIQDVAAYV CYC6_SYNLI 55 31
KNAMPAFGGRLVDEDIEDAANYV CYC6_PORPU 80 31
KNAMPAFGGRLVDEDIEDAANYV CYC6_PORTE 55 31
QGAMPAFGGRLSDADIANVAAYI CYC6_SYNP2 86 38
KNAMPAFKGRLKPEQIEDVAAYV CYC6_ANASP 80 31
KGAMPAWDGRLDEDEIAGVAAYV CYC6_MONBR 58 33
KNAMPGFNGRLSPKQIEDVAAYV CYC6_SPIMA 59 35
KNAMPAFKGRLKPDQIEDVAAYV CYC6_ANASQ 80 31
MGAMPAFGGRLSAEDIEAVANYV CYC6_MICAE 51 31
KGAMPAFKGRLSDDQIQSVALYV CYC6_PLEBO 55 31
KNAMPAFGGRLSETDIEDVANFV CYC6_PETFA 55 31
KGAMPAFGIRLKAEQIENVAAYV CYC6_APHFL 55 31
KGAMPAFGSKLSADDIADVASYV CYC6_SYNP7 79 31
KNAMPAFKGRLKPEEIZBVAAYV CYC6_ANAVA 55 31
KGAMPAWADRLSEEEIQAVAEYV CYC6_CHLRE 115 33
KGAMPAWSDRLDDEEIDGVVAYV CYC6_BRYMA 58 33
KNAMPAFGSRLAETDIEDVANFV CYC6_ALAES 55 31
KGAMPAFGAKLSADDIEGVASYA CYC6_ANANI 55 31
NGAMPGFKGRISDSDMEDVAAYV CYC6_SYNY3 90 31
KNAMPAFGGRLEDDEIANVASYV CYC6_MONLU 56 32
GGVMPAWGPRLSPTTIKALTVYV Q43945 264 127
FGVMPAWTGRLSEADIVAVAAYV Q51682 319 129
FGVMPNWNARLTEADIRSVAVYV Q53114 261 32
AGVMPAWEGRLDPSTIKAMAVYV Q03075 261 32
KGPMPAWEGVLSEDEIVAVTDYV CYC6_EUGGR 53 33
KGPMPAWEGVLDESEIKEVTDYV CYC6_EUGVI 53 33
HGVMPAWLPRLGDDTVKQLAVFV Q05577 260 32
HGVMPAWAGRLGDTTVKELTIFV P72287 258 32
SWAADGAKPRLSEAQIRAVASYV Q52689 268 39
HGVMPAWAARLGDTTVNELTNFV O69780 258 127
VLEMTGMLDPLSDQDLEDIAAYF CYC4_PSEST 83 39
SWAADGAKPRLSEAQIRAVASYV O30730 268 137
AVAMPGFKNHLSDQEMADVVNFM CYCA_GLUSU 391 41
AITMPAFGWRLNDQQVADVVNFI O34215 377 42
VLEMTGLLTNLSNEDLADIAAYF CYC4_PSEAE 54 30
AALMTPMAQGLSDEDIADIAAYY C554_PARSP 57 33
VLEMTGMLDNFSDQDLADLAAYF CYC4_AZOVI 83 39
AVAMPGYSKSLSAQQIADVVNFI CYCA_ACEPO 381 41
VRGMPDFTGKLSGDDVESLKAFI Q46444 675 30
AVAMPDYKNILSDQQIADVVNFI Q57536 382 41
KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 77 34
KGMMERVVKSLTDEDIEVLATHI C553_DESDN 55 32
GNKMTGTYPKLSDSETNALYEYL O34404 326 45
GNKMTGTYPKLSDSETNALYEYL COX2_BACSU 326 45
STVMGRHAKGYSDEEIHQIAEYF CYSD_CHLLT 57 29
KAMMTNAVKKYSDEELKALADYM C553_DESVH 78 34
SAIMAPNAAGLSEQDMDNLSAYI C554_THINE 65 40
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