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Protein

Cytochrome c-553

Gene

cyf

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Natural electron acceptor for a formate dehydrogenase.

Redox potential

E0 is about +10 mV.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei34 – 341Heme (covalent)
Binding sitei37 – 371Heme (covalent)
Metal bindingi38 – 381Iron (heme axial ligand)
Metal bindingi81 – 811Iron (heme axial ligand)

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciDVUL882:GJIL-1858-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytochrome c-553
Alternative name(s):
Cytochrome c553
Low-potential cytochrome c
Gene namesi
Name:cyf
Ordered Locus Names:DVU_1817
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002194 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 24241 PublicationAdd
BLAST
Chaini25 – 10379Cytochrome c-5531 PublicationPRO_0000006535Add
BLAST

Post-translational modificationi

Binds 1 heme group per subunit.

Proteomic databases

PaxDbiP04032.

Interactioni

Protein-protein interaction databases

MINTiMINT-365255.
STRINGi882.DVU1817.

Structurei

Secondary structure

1
103
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi27 – 315Combined sources
Helixi32 – 343Combined sources
Helixi35 – 384Combined sources
Turni39 – 424Combined sources
Turni47 – 493Combined sources
Helixi58 – 7013Combined sources
Helixi78 – 858Combined sources
Helixi90 – 10213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DVHNMR-A25-103[»]
1DWLNMR-B25-103[»]
1E08NMR-E26-103[»]
2DVHNMR-A25-103[»]
ProteinModelPortaliP04032.
SMRiP04032. Positions 25-103.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04032.

Family & Domainsi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105VBD. Bacteria.
ENOG410XUC7. LUCA.
KOiK08738.
OMAiTALKGYK.
OrthoDBiEOG6PGK4H.
PhylomeDBiP04032.

Family and domain databases

Gene3Di1.10.760.10. 1 hit.
InterProiIPR009056. Cyt_c-like_dom.
[Graphical view]
PfamiPF00034. Cytochrom_C. 1 hit.
[Graphical view]
SUPFAMiSSF46626. SSF46626. 1 hit.
PROSITEiPS51007. CYTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04032-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKRVLLLSSL CAALSFGLAV SGVAADGAAL YKSCIGCHGA DGSKAAMGSA
60 70 80 90 100
KPVKGQGAEE LYKKMKGYAD GSYGGERKAM MTNAVKKYSD EELKALADYM

SKL
Length:103
Mass (Da):10,692
Last modified:January 1, 1990 - v2
Checksum:i0AD6AA6408505DA4
GO

Sequence cautioni

The sequence described in PubMed:5038698 differs from that shown.A number of tryptic peptides were mixed up.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti39 – 391G → S AA sequence (PubMed:5038698).Curated
Sequence conflicti43 – 431S → G AA sequence (PubMed:5038698).Curated
Sequence conflicti64 – 641Missing AA sequence (PubMed:5038698).Curated
Sequence conflicti87 – 871K → GK AA sequence (PubMed:5038698).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27062 Genomic DNA. Translation: AAA23356.1.
L25251 Unassigned DNA. Translation: AAA16453.1.
AE017285 Genomic DNA. Translation: AAS96294.1.
PIRiA44752.
RefSeqiWP_010939104.1. NC_002937.3.
YP_011035.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS96294; AAS96294; DVU_1817.
GeneIDi2796646.
KEGGidvu:DVU1817.
PATRICi32063388. VBIDesVul119526_1667.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27062 Genomic DNA. Translation: AAA23356.1.
L25251 Unassigned DNA. Translation: AAA16453.1.
AE017285 Genomic DNA. Translation: AAS96294.1.
PIRiA44752.
RefSeqiWP_010939104.1. NC_002937.3.
YP_011035.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DVHNMR-A25-103[»]
1DWLNMR-B25-103[»]
1E08NMR-E26-103[»]
2DVHNMR-A25-103[»]
ProteinModelPortaliP04032.
SMRiP04032. Positions 25-103.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-365255.
STRINGi882.DVU1817.

Proteomic databases

PaxDbiP04032.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS96294; AAS96294; DVU_1817.
GeneIDi2796646.
KEGGidvu:DVU1817.
PATRICi32063388. VBIDesVul119526_1667.

Phylogenomic databases

eggNOGiENOG4105VBD. Bacteria.
ENOG410XUC7. LUCA.
KOiK08738.
OMAiTALKGYK.
OrthoDBiEOG6PGK4H.
PhylomeDBiP04032.

Enzyme and pathway databases

BioCyciDVUL882:GJIL-1858-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP04032.

Family and domain databases

Gene3Di1.10.760.10. 1 hit.
InterProiIPR009056. Cyt_c-like_dom.
[Graphical view]
PfamiPF00034. Cytochrom_C. 1 hit.
[Graphical view]
SUPFAMiSSF46626. SSF46626. 1 hit.
PROSITEiPS51007. CYTC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the gene encoding cytochrome c553 from Desulfovibrio vulgaris Hildenborough."
    van Rooijen G.J.H., Bruschi M., Voordouw G.
    J. Bacteriol. 171:3575-3578(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR."
    Blanchard L., Marion D., Pollock B., Voordouw G., Wall J., Bruschi M., Guerlesquin F.
    Eur. J. Biochem. 218:293-301(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
  4. "C-type cytochromes of Desulfovibrio vulgaris. The primary structure of cytochrome c 553."
    Bruschi M., le Gall J.
    Biochim. Biophys. Acta 271:48-60(1972) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 25-103.
  5. "Sequential NMR resonance assignment and secondary structure of ferrocytochrome c553 from Desulfovibrio vulgaris Hildenborough."
    Marion D., Guerlesquin F.
    Biochemistry 31:8171-8179(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  6. "Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics."
    Blackledge M.J., Medvedeva S., Poncin M., Guerlesquin F., Bruschi M., Marion D.
    J. Mol. Biol. 245:661-681(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  7. "Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c553 by two-dimensional H-NMR spectra."
    Blanchard L., Blackledge M.J., Marion D., Guerlesquin F.
    FEBS Lett. 389:203-209(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  8. "1H-NMR study of the structural influence of Y64 substitution in Desulfovibrio vulgaris Hildenborough cytochrome c553."
    Sebban-Kreuzer C., Blanchard L., Bersch B., Blackledge M.J., Marion D., Dolla A., Guerlesquin F.
    Eur. J. Biochem. 251:787-794(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF MUTANTS OF TYR-88.
  9. "Tyrosine 64 of cytochrome c553 is required for electron exchange with formate dehydrogenase in Desulfovibrio vulgaris Hildenborough."
    Sebban-Kreuzer C., Blackledge M., Dolla A., Marion D., Guerlesquin F.
    Biochemistry 37:8331-8340(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF MUTANT OF TYR-88.
  10. "The formate dehydrogenase-cytochrome c553 complex from Desulfovibrio vulgaris Hildenborough."
    Sebban-Kreuzer C., Dolla A., Guerlesquin F.
    Eur. J. Biochem. 253:645-652(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF MUTANTS OF LYS-63 AND LYS-64.

Entry informationi

Entry nameiCY553_DESVH
AccessioniPrimary (citable) accession number: P04032
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: January 1, 1990
Last modified: November 11, 2015
This is version 136 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.