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Protein

Cytochrome c3

Gene

DvMF_2499

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi45 – 451Iron (heme 1 axial ligand)
Metal bindingi48 – 481Iron (heme 3 axial ligand)
Binding sitei53 – 531Heme 1 (covalent)
Binding sitei56 – 561Heme 1 (covalent)
Metal bindingi57 – 571Iron (heme 1 axial ligand)
Metal bindingi58 – 581Iron (heme 2 axial ligand)
Binding sitei69 – 691Heme 2 (covalent); atypical
Binding sitei74 – 741Heme 2 (covalent); atypical
Metal bindingi75 – 751Iron (heme 2 axial ligand)
Metal bindingi93 – 931Iron (heme 4 axial ligand)
Binding sitei102 – 1021Heme 3 (covalent)
Binding sitei105 – 1051Heme 3 (covalent)
Metal bindingi106 – 1061Iron (heme 3 axial ligand)
Binding sitei123 – 1231Heme 4 (covalent); atypical
Binding sitei128 – 1281Heme 4 (covalent); atypical
Metal bindingi129 – 1291Iron (heme 4 axial ligand)

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Electron transport, Sulfate respiration, Transport

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-2569-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytochrome c3
Gene namesi
Ordered Locus Names:DvMF_2499
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000001361 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 – 23231 PublicationAdd
BLAST
Chaini24 – 130107Cytochrome c3PRO_0000006505Add
BLAST

Post-translational modificationi

Binds 4 heme groups per subunit.

Interactioni

Protein-protein interaction databases

STRINGi883.DvMF_2499.

Structurei

Secondary structure

1
130
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi32 – 343Combined sources
Beta strandi36 – 394Combined sources
Beta strandi41 – 433Combined sources
Helixi45 – 473Combined sources
Turni48 – 503Combined sources
Helixi53 – 553Combined sources
Helixi88 – 936Combined sources
Beta strandi95 – 995Combined sources
Helixi102 – 1109Combined sources
Helixi114 – 1218Combined sources
Beta strandi123 – 1286Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IT1NMR-A24-130[»]
1J0OX-ray1.15A24-130[»]
1J0PX-ray0.91A23-130[»]
1WR5X-ray1.40A23-130[»]
2CDVX-ray1.80A24-130[»]
2EWIX-ray1.00A24-130[»]
2EWKX-ray1.00A24-130[»]
2EWUX-ray1.10A24-130[»]
2FFNX-ray1.80A24-130[»]
2YXCX-ray1.50A24-130[»]
2YYWX-ray1.33A24-130[»]
2YYXX-ray1.00A24-130[»]
2Z47X-ray1.60A/B24-130[»]
ProteinModelPortaliP00132.
SMRiP00132. Positions 24-130.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00132.

Family & Domainsi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4106BES. Bacteria.
ENOG410XXW1. LUCA.
HOGENOMiHOG000136348.
OMAiKELTGCK.
OrthoDBiEOG6Q2SNC.

Family and domain databases

InterProiIPR002322. Cyt_c_III.
IPR020942. Cyt_c_III_dom.
IPR011031. Multihaem_cyt.
[Graphical view]
PfamiPF02085. Cytochrom_CIII. 1 hit.
[Graphical view]
PRINTSiPR00609. CYTOCHROMEC3.
SUPFAMiSSF48695. SSF48695. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P00132-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKMFLTGVL ALAVAIAMPA LAAAPKAPAD GLKMDKTKQP VVFNHSTHKA
60 70 80 90 100
VKCGDCHHPV NGKEDYQKCA TAGCHDNMDK KDKSAKGYYH AMHDKGTKFK
110 120 130
SCVGCHLETA GADAAKKKEL TGCKGSKCHS
Length:130
Mass (Da):13,843
Last modified:July 15, 1998 - v2
Checksum:iCCBBA60351B9EF8E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti65 – 651D → N AA sequence (PubMed:6249799).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31702 Genomic DNA. Translation: BAA06511.1.
CP001197 Genomic DNA. Translation: ACL09439.1.
PIRiS33874. CCDV3M.
RefSeqiWP_015946129.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL09439; ACL09439; DvMF_2499.
KEGGidvm:DvMF_2499.
PATRICi21775419. VBIDesVul86729_2712.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31702 Genomic DNA. Translation: BAA06511.1.
CP001197 Genomic DNA. Translation: ACL09439.1.
PIRiS33874. CCDV3M.
RefSeqiWP_015946129.1. NC_011769.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IT1NMR-A24-130[»]
1J0OX-ray1.15A24-130[»]
1J0PX-ray0.91A23-130[»]
1WR5X-ray1.40A23-130[»]
2CDVX-ray1.80A24-130[»]
2EWIX-ray1.00A24-130[»]
2EWKX-ray1.00A24-130[»]
2EWUX-ray1.10A24-130[»]
2FFNX-ray1.80A24-130[»]
2YXCX-ray1.50A24-130[»]
2YYWX-ray1.33A24-130[»]
2YYXX-ray1.00A24-130[»]
2Z47X-ray1.60A/B24-130[»]
ProteinModelPortaliP00132.
SMRiP00132. Positions 24-130.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi883.DvMF_2499.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL09439; ACL09439; DvMF_2499.
KEGGidvm:DvMF_2499.
PATRICi21775419. VBIDesVul86729_2712.

Phylogenomic databases

eggNOGiENOG4106BES. Bacteria.
ENOG410XXW1. LUCA.
HOGENOMiHOG000136348.
OMAiKELTGCK.
OrthoDBiEOG6Q2SNC.

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-2569-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP00132.

Family and domain databases

InterProiIPR002322. Cyt_c_III.
IPR020942. Cyt_c_III_dom.
IPR011031. Multihaem_cyt.
[Graphical view]
PfamiPF02085. Cytochrom_CIII. 1 hit.
[Graphical view]
PRINTSiPR00609. CYTOCHROMEC3.
SUPFAMiSSF48695. SSF48695. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The primary structure of pre-cytochrome c(3) from Desulfovibrio vulgaris (Miyazaki F) as determined by nucleotide sequencing of its gene and partial amino acid sequencing."
    Kitamura M., Ozawa K., Kojima S., Kumagai I., Akutsu H., Miura K.I.
    Protein Seq. Data Anal. 5:193-196(1993)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
    Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Miyazaki F / DSM 19637.
  3. "Amino acid sequence of cytochrome c3 from Desulfovibrio vulgaris, Miyazaki."
    Shinkai W., Hase T., Yagi T., Matsubara H.
    J. Biochem. 87:1747-1756(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 24-130.
  4. "The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki at 2.5-A resolution."
    Higuchi Y., Bando S., Kusunoki M., Matsuura Y., Yasuoka N., Kakudo M., Yamanaka T., Yagi T., Inokuchi H.
    J. Biochem. 89:1659-1662(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  5. "1H NMR studies on ferricytochrome c3 from Desulfovibrio vulgaris Miyazaki F and its interaction with ferredoxin I."
    Park J.-S., Kano K., Morimoto Y., Higuchi Y., Yasuoka N., Ogata M., Niki K., Akutsu H.
    J. Biomol. NMR 1:271-282(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.

Entry informationi

Entry nameiCYC3_DESVM
AccessioniPrimary (citable) accession number: P00132
Secondary accession number(s): B8DMZ9, Q46607
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 15, 1998
Last modified: January 20, 2016
This is version 119 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The second and fourth heme binding sites have unusual CXXXXCH motifs.

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.