SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR00605

Identifier
CYTCHROMECIC  [View Relations]  [View Alignment]  
Accession
PR00605
No. of Motifs
2
Creation Date
09-JUL-1996  (UPDATE 14-JUN-1999)
Title
Class IC cytochrome C signature
Database References

PROSITE; PS00190 CYTOCHROME_C
BLOCKS; BL00190
INTERPRO; IPR002329
PDB; 1C53; 1CYI
SCOP; 1C53; 1CYI
CATH; 1C53; 1CYI
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. KERFELD, C.A., ANWAR, H.P., INTERRANTE, R., MERCHANT, S. AND YEATES, T.O.
The structure of chloroplast cytochrome c6 at 1.9 A 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.BIOCHEMISTRY 108 701-703 (1990).

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 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 Feature Index
25050
12
True Positives
C553_DESDN    C553_DESVH    C553_DESVM    C554_PARSP    
C554_THINE COX2_BACSU CYC4_AZOVI CYC4_PSEAE
CYC4_PSEST CYC6_ALAES CYC6_ANANI CYC6_ANASP
CYC6_ANASQ CYC6_ANAVA CYC6_APHFL CYC6_BRYMA
CYC6_BUMFI CYC6_CHLRE CYC6_EUGGR CYC6_EUGVI
CYC6_MICAE CYC6_MONBR CYC6_MONLU CYC6_PETFA
CYC6_PLEBO CYC6_PORPU CYC6_PORTE CYC6_SPIMA
CYC6_SYNEN CYC6_SYNLI CYC6_SYNP2 CYC6_SYNP7
CYC6_SYNSP CYC6_SYNY3 CYCA_ACEPO CYCA_GLUSU
CYSD_CHLLT O30730 O34215 O34404
O69780 P72287 Q03075 Q05577
Q43945 Q46444 Q51682 Q52689
Q53114 Q57536
Sequence Titles
C553_DESDN  CYTOCHROME C-553 (C553) - DESULFOVIBRIO DESULFURICANS (STRAIN NORWAY 4). 
C553_DESVH CYTOCHROME C-553 PRECURSOR (C553) (LOW POTENTIAL CYTOCHROME C) - DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH).
C553_DESVM CYTOCHROME C-553 PRECURSOR (C553) - DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI).
C554_PARSP CYTOCHROME C-554(548) (C554) - PARACOCCUS SP. (STRAIN ATCC 12084).
C554_THINE CYTOCHROME C-554(547) (C554) - THIOBACILLUS NEAPOLITANUS.
COX2_BACSU CYTOCHROME C OXIDASE POLYPEPTIDE II PRECURSOR (EC 1.9.3.1) (CYTOCHROME AA3 SUBUN
CYC4_AZOVI CYTOCHROME C4 PRECURSOR - AZOTOBACTER VINELANDII.
CYC4_PSEAE CYTOCHROME C4 - PSEUDOMONAS AERUGINOSA.
CYC4_PSEST CYTOCHROME C4 PRECURSOR - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
CYC6_ALAES CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ALARIA ESCULENTA (ATLANTIC WAKAME) (BADDERLOCKS).
CYC6_ANANI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANACYSTIS NIDULANS.
CYC6_ANASP CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA SP. (STRAIN PCC 7120).
CYC6_ANASQ CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA SP. (STRAIN PCC 7937).
CYC6_ANAVA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA VARIABILIS.
CYC6_APHFL CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - APHANIZOMENON FLOS-AQUAE.
CYC6_BRYMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BRYOPSIS MAXIMA.
CYC6_BUMFI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BUMILLERIOPSIS FILIFORMIS.
CYC6_CHLRE CYTOCHROME C6 PRECURSOR (CYTOCHROME C552) - CHLAMYDOMONAS REINHARDTII.
CYC6_EUGGR CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUGLENA GRACILIS.
CYC6_EUGVI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUGLENA VIRIDIS.
CYC6_MICAE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - MICROCYSTIS AERUGINOSA.
CYC6_MONBR CYTOCHROME C6 (CYTOCHROME C552) - MONORAPHIDIUM BRAUNII.
CYC6_MONLU CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PAVLOVA LUTHERII (MONOCHRYSIS LUTHERI).
CYC6_PETFA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PETALONIA FASCIA (KELP).
CYC6_PLEBO CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PLECTONEMA BORYANUM.
CYC6_PORPU CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PORPHYRA PURPUREA.
CYC6_PORTE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PORPHYRA TENERA.
CYC6_SPIMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SPIRULINA MAXIMA.
CYC6_SYNEN CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS ELONGATUS NAEGELI.
CYC6_SYNLI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS LIVIDUS.
CYC6_SYNP2 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. (STRAIN PCC 7002) (AGMENELLUM QUADRUPLICATUM).
CYC6_SYNP7 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
CYC6_SYNSP CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP.
CYC6_SYNY3 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
CYCA_ACEPO ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR - ACETOBACTER POLYOXOGENES, AND ACETOBACTER EUROPAEUS.
CYCA_GLUSU ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR (CYTOCHROME C- 553) (C553) (G3-ADH SUBUNIT II) - GLUCONOBACTER SUBOXYDANS.
CYSD_CHLLT CYTOCHROME SUBUNIT OF SULFIDE DEHYDROGENASE (FC) (FCSD) (FLAVOCYTOCHROME C CYTOCHROME SUBUNIT) - CHLOROBIUM LIMICOLA F.SP. THIOSULFATOPHILUM.
O30730 DI-HEME CYTOCHROME CP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O34215 CYTOCHROME C PRECURSOR - ERWINIA CYPRIPEDII.
O34404 CYTOCHROME C OXIDASE POLYPEPTIDE II (EC 1.9.3.1) - BACILLUS SUBTILIS.
O69780 DI-HEME CYTOCHROME C - RHIZOBIUM ETLI.
P72287 FIXPC - RHIZOBIUM LEGUMINOSARUM.
Q03075 CYTOCHROME C - BRADYRHIZOBIUM JAPONICUM.
Q05577 FIXP PROTEIN - RHIZOBIUM MELILOTI.
Q43945 GENES FIXN, FIXO, FIXQ, FIXP AND FIXG - AZORHIZOBIUM CAULINODANS.
Q46444 QUINOHAEMOPROTEIN ETHANOL DEHYDROGENASE TYPE I PRECURSOR (EC 1.1.99.-) (QH-EDH1) - COMAMONAS TESTOSTERONI (PSEUDOMONAS TESTOSTERONI).
Q51682 CCOP - PARACOCCUS DENITRIFICANS.
Q52689 CCOP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
Q53114 CBB3-TYPE CYTOCHROME C OXIDASE CCOP SUBUNIT - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
Q57536 CYTOCHROME C SUBUNIT OF ALCOHOL DEHYDROGENASE - ACETOBACTER PASTEURIANUS.
Scan History
OWL28_0    2  160  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
AVCGACHGVDGN PSU05988 32 32 -
ANCAACHAGGNN CYC6_PORTE 12 12 -
ANCASCHAGGKN CYC6_ANASP 37 37 -
ANCASCHMGGKN CYC6_MICAE 8 8 -
ANCAACHASGGG CYC6_PLEBO 12 12 -
ANCAQCHVGGGN CYC6_APHFL 12 12 -
GNCAACHMGGRN CYC6_CHLRE 70 70 -
GNCAACHAGGAN CYC6_BRYMA 13 13 -
ANCSACHAGGNN CYC6_ALAES 12 12 -
GNCAACHNGGLN CYC6_SYNY3 47 47 -
NNCSSCHVNGGN CYC6_EUGVI 8 8 -
AVCGACHGADGN CYC4_PSEAE 12 12 -
GTCVACHGTDGQ C554_PARSP 12 12 -
AVCGACHGPDGN CYC4_AZOVI 12 12 -
KSCVGCHGADGS C553_DESVM 8 8 -
KMCKSCHGADGS C553_DESDN 11 11 -
ASCASCHGMQAQ C554_THINE 13 13 -

Motif 2 width=23
Element Seqn Id St Int Rpt
SAIMAPNAAGLSEQDMDNLSAYI C554_THINE 65 40 -
VLEMTGMLDPLSDQDLEDIAAYF PSU05988 83 39 -
KNAMPAFGGRLVDEDIEDAANYV CYC6_PORTE 55 31 -
KNAMPAFKGRLKPEQIEDVAAYV CYC6_ANASP 80 31 -
MGAMPAFGGRLSAEDIEAVANYV CYC6_MICAE 51 31 -
KGAMPAFKGRLSDDQIQSVALYV CYC6_PLEBO 55 31 -
KGAMPAFGIRLKAEQIENVAAYV CYC6_APHFL 55 31 -
KGAMPAWADRLSEEEIQAVAEYV CYC6_CHLRE 115 33 -
KGAMPAWSDRLDDEEIDGVVAYV CYC6_BRYMA 58 33 -
KNAMPAFGSRLAETDIEDVANFV CYC6_ALAES 55 31 -
NGAMPGFKGRISDSDMEDVAAYV CYC6_SYNY3 90 31 -
KGPMPAWEGVLDESEIKEVTDYV CYC6_EUGVI 53 33 -
VLEMTGLLTNLSNEDLADIAAYF CYC4_PSEAE 54 30 -
AALMTPMAQGLSDEDIADIAAYY C554_PARSP 57 33 -
VLEMTGMLDNFSDQDLADLAAYF CYC4_AZOVI 63 39 -
KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 54 34 -
KGMMERVVKSLTDEDIEVLATHI C553_DESDN 55 32 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
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 12 12 -
KECAICHRNDGG CYCA_ACEPO 328 328 -
ANCVFCHGVPGV Q46444 633 633 -
EQCAICHRNDGG Q57536 329 329 -
KSCVGCHGADGS C553_DESVM 8 8 -
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 -

Motif 2 width=23
Element Seqn Id St Int Rpt
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 63 39 -
AVAMPGYSKSLSAQQIADVVNFI CYCA_ACEPO 381 41 -
VRGMPDFTGKLSGDDVESLKAFI Q46444 675 30 -
AVAMPDYKNILSDQQIADVVNFI Q57536 382 41 -
KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 54 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 -