P00132 (CYC3_DESVM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cytochrome c3

Gene names

Ordered Locus Names:

DvMF_2499

Organism

Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [Complete proteome] [HAMAP]

Taxonomic identifier

883 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio › Desulfovibrio vulgaris

Protein attributes

Sequence length	130 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
Subcellular location	Periplasm.
Post-translational modification	Binds 4 heme groups per subunit.
Miscellaneous	The second and fourth heme binding sites have unusual CXXXXCH motifs.

Ontologies

Keywords
Biological process	Electron transport Sulfate respiration Transport
Cellular component	Periplasm
Domain	Signal
Ligand	Heme Iron Metal-binding
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological_process	anaerobic respiration Inferred from electronic annotation. Source: UniProtKB-KW electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	electron carrier activity Inferred from electronic annotation. Source: InterPro heme binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 23

23

Ref.3

Chain

24 – 130

107

Cytochrome c3

PRO_0000006505

Sites

Metal binding

45

1

Iron (heme 1 axial ligand)

Metal binding

48

1

Iron (heme 3 axial ligand)

Metal binding

57

1

Iron (heme 1 axial ligand)

Metal binding

58

1

Iron (heme 2 axial ligand)

Metal binding

75

1

Iron (heme 2 axial ligand)

Metal binding

93

1

Iron (heme 4 axial ligand)

Metal binding

106

1

Iron (heme 3 axial ligand)

Metal binding

129

1

Iron (heme 4 axial ligand)

Binding site

53

1

Heme 1 (covalent)

Binding site

56

1

Heme 1 (covalent)

Binding site

69

1

Heme 2 (covalent); atypical

Binding site

74

1

Heme 2 (covalent); atypical

Binding site

102

1

Heme 3 (covalent)

Binding site

105

1

Heme 3 (covalent)

Binding site

123

1

Heme 4 (covalent); atypical

Binding site

128

1

Heme 4 (covalent); atypical

Experimental info

Sequence conflict

65

1

D → N AA sequence Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

130

Helix Strand Turn

Details...

Beta strand

32 – 34

3

Beta strand

36 – 39

4

Beta strand

41 – 43

3

Helix

45 – 47

3

Turn

48 – 50

3

Helix

53 – 55

3

Helix

88 – 93

6

Beta strand

95 – 99

5

Helix

102 – 110

9

Helix

114 – 121

8

Beta strand

123 – 128

6

Sequences

	Sequence		Length	Mass (Da)
	P00132 [UniParc]. Last modified July 15, 1998. Version 2. Checksum: CCBBA60351B9EF8E	FASTA	130	13,843
	10 20 30 40 50 60 MKKMFLTGVL ALAVAIAMPA LAAAPKAPAD GLKMDKTKQP VVFNHSTHKA VKCGDCHHPV 70 80 90 100 110 120 NGKEDYQKCA TAGCHDNMDK KDKSAKGYYH AMHDKGTKFK SCVGCHLETA GADAAKKKEL 130 TGCKGSKCHS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D31702 Genomic DNA. Translation: BAA06511.1.
CP001197 Genomic DNA. Translation: ACL09439.1.

PIR

CCDV3M. S33874.

RefSeq

YP_002436907.1. NC_011769.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IT1	NMR	-	A	24-130	[»]
1J0O	X-ray	1.15	A	24-130	[»]
1J0P	X-ray	0.91	A	23-130	[»]
1WR5	X-ray	1.40	A	23-130	[»]
2CDV	X-ray	1.80	A	24-130	[»]
2EWI	X-ray	1.00	A	24-130	[»]
2EWK	X-ray	1.00	A	24-130	[»]
2EWU	X-ray	1.10	A	24-130	[»]
2FFN	X-ray	1.80	A	24-130	[»]
2YXC	X-ray	1.50	A	24-130	[»]
2YYW	X-ray	1.33	A	24-130	[»]
2YYX	X-ray	1.00	A	24-130	[»]
2Z47	X-ray	1.60	A/B	24-130	[»]

ProteinModelPortal

P00132.

SMR

P00132. Positions 24-130.

ModBase

Search...

Protein-protein interaction databases

STRING

883.DvMF_2499.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ACL09439; ACL09439; DvMF_2499.

GeneID

7174435.

KEGG

dvm:DvMF_2499.

PATRIC

21775419. VBIDesVul86729_2712.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

NOG68495.

HOGENOM

HOG000136348.

OMA

KELTGCK.

ProtClustDB

CLSK926806.

Enzyme and pathway databases

BioCyc

DVUL883:GCJ5-2569-MONOMER.

Family and domain databases

InterPro

IPR002322. Cyt_c_III.
IPR020942. Cyt_c_III_dom.
[Graphical view]

Pfam

PF02085. Cytochrom_CIII. 1 hit.
[Graphical view]

PRINTS

PR00609. CYTOCHROMEC3.

PROSITE

PS51008. MULTIHEME_CYTC. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00132.

Entry information

Entry name

CYC3_DESVM

Accession

Primary (citable) accession number: P00132
Secondary accession number(s): B8DMZ9, Q46607

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 15, 1998
Last modified:	May 29, 2013
This is version 103 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program