CYC3_DESVM
ID CYC3_DESVM Reviewed; 130 AA.
AC P00132; B8DMZ9; Q46607;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Cytochrome c3;
DE Flags: Precursor;
GN OrderedLocusNames=DvMF_2499;
OS Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Desulfovibrio.
OX NCBI_TaxID=883;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Kitamura M., Ozawa K., Kojima S., Kumagai I., Akutsu H., Miura K.I.;
RT "The primary structure of pre-cytochrome c(3) from Desulfovibrio vulgaris
RT (Miyazaki F) as determined by nucleotide sequencing of its gene and partial
RT amino acid sequencing.";
RL Protein Seq. Data Anal. 5:193-196(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 19637 / Miyazaki F;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C.,
RA Richardson P.;
RT "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'.";
RL Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROTEIN SEQUENCE OF 24-130.
RX PubMed=6249799; DOI=10.1093/oxfordjournals.jbchem.a132919;
RA Shinkai W., Hase T., Yagi T., Matsubara H.;
RT "Amino acid sequence of cytochrome c3 from Desulfovibrio vulgaris,
RT Miyazaki.";
RL J. Biochem. 87:1747-1756(1980).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=6268619; DOI=10.1093/oxfordjournals.jbchem.a133364;
RA Higuchi Y., Bando S., Kusunoki M., Matsuura Y., Yasuoka N., Kakudo M.,
RA Yamanaka T., Yagi T., Inokuchi H.;
RT "The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki at
RT 2.5-A resolution.";
RL J. Biochem. 89:1659-1662(1981).
RN [5]
RP STRUCTURE BY NMR.
RX PubMed=1668723; DOI=10.1007/bf01875520;
RA Park J.-S., Kano K., Morimoto Y., Higuchi Y., Yasuoka N., Ogata M.,
RA Niki K., Akutsu H.;
RT "1H NMR studies on ferricytochrome c3 from Desulfovibrio vulgaris Miyazaki
RT F and its interaction with ferredoxin I.";
RL J. Biomol. NMR 1:271-282(1991).
CC -!- FUNCTION: Participates in sulfate respiration coupled with
CC phosphorylation by transferring electrons from the enzyme dehydrogenase
CC to ferredoxin.
CC -!- SUBCELLULAR LOCATION: Periplasm.
CC -!- PTM: Binds 4 heme c groups per subunit.
CC -!- MISCELLANEOUS: The second and fourth heme binding sites have unusual
CC CXXXXCH motifs.
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DR EMBL; D31702; BAA06511.1; -; Genomic_DNA.
DR EMBL; CP001197; ACL09439.1; -; Genomic_DNA.
DR PIR; S33874; CCDV3M.
DR RefSeq; WP_015946129.1; NC_011769.1.
DR PDB; 1IT1; NMR; -; A=24-130.
DR PDB; 1J0O; X-ray; 1.15 A; A=24-130.
DR PDB; 1J0P; X-ray; 0.91 A; A=23-130.
DR PDB; 1WR5; X-ray; 1.40 A; A=23-130.
DR PDB; 2CDV; X-ray; 1.80 A; A=24-130.
DR PDB; 2EWI; X-ray; 1.00 A; A=24-130.
DR PDB; 2EWK; X-ray; 1.00 A; A=24-130.
DR PDB; 2EWU; X-ray; 1.10 A; A=24-130.
DR PDB; 2FFN; X-ray; 1.80 A; A=24-130.
DR PDB; 2YXC; X-ray; 1.50 A; A=24-130.
DR PDB; 2YYW; X-ray; 1.33 A; A=24-130.
DR PDB; 2YYX; X-ray; 1.00 A; A=24-130.
DR PDB; 2Z47; X-ray; 1.60 A; A/B=24-130.
DR PDBsum; 1IT1; -.
DR PDBsum; 1J0O; -.
DR PDBsum; 1J0P; -.
DR PDBsum; 1WR5; -.
DR PDBsum; 2CDV; -.
DR PDBsum; 2EWI; -.
DR PDBsum; 2EWK; -.
DR PDBsum; 2EWU; -.
DR PDBsum; 2FFN; -.
DR PDBsum; 2YXC; -.
DR PDBsum; 2YYW; -.
DR PDBsum; 2YYX; -.
DR PDBsum; 2Z47; -.
DR AlphaFoldDB; P00132; -.
DR BMRB; P00132; -.
DR SMR; P00132; -.
DR STRING; 883.DvMF_2499; -.
DR DrugBank; DB03317; Ferroheme C.
DR EnsemblBacteria; ACL09439; ACL09439; DvMF_2499.
DR KEGG; dvm:DvMF_2499; -.
DR eggNOG; ENOG503407D; Bacteria.
DR HOGENOM; CLU_125874_3_0_7; -.
DR OMA; KELTGCK; -.
DR OrthoDB; 738283at2; -.
DR EvolutionaryTrace; P00132; -.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009061; P:anaerobic respiration; IEA:UniProtKB-KW.
DR InterPro; IPR002322; Cyt_c_III.
DR InterPro; IPR020942; Cyt_c_III_dom.
DR InterPro; IPR036280; Multihaem_cyt_sf.
DR Pfam; PF02085; Cytochrom_CIII; 1.
DR PRINTS; PR00609; CYTOCHROMEC3.
DR SUPFAM; SSF48695; SSF48695; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Electron transport; Heme; Iron;
KW Metal-binding; Periplasm; Signal; Sulfate respiration; Transport.
FT SIGNAL 1..23
FT /evidence="ECO:0000269|PubMed:6249799"
FT CHAIN 24..130
FT /note="Cytochrome c3"
FT /id="PRO_0000006505"
FT BINDING 45
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 48
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 53
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /note="covalent"
FT BINDING 56
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /note="covalent"
FT BINDING 57
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 58
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 69
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /note="covalent"
FT BINDING 74
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /note="covalent"
FT BINDING 75
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 93
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 102
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /note="covalent"
FT BINDING 105
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /note="covalent"
FT BINDING 106
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT BINDING 123
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /note="covalent"
FT BINDING 128
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /note="covalent"
FT BINDING 129
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT CONFLICT 65
FT /note="D -> N (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:1J0P"
FT STRAND 36..39
FT /evidence="ECO:0007829|PDB:1J0P"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:1J0P"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:1J0P"
FT TURN 48..50
FT /evidence="ECO:0007829|PDB:1IT1"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:1J0P"
FT HELIX 88..93
FT /evidence="ECO:0007829|PDB:1J0P"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:1IT1"
FT HELIX 102..110
FT /evidence="ECO:0007829|PDB:1J0P"
FT HELIX 114..121
FT /evidence="ECO:0007829|PDB:1J0P"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:1J0P"
SQ SEQUENCE 130 AA; 13843 MW; CCBBA60351B9EF8E CRC64;
MKKMFLTGVL ALAVAIAMPA LAAAPKAPAD GLKMDKTKQP VVFNHSTHKA VKCGDCHHPV
NGKEDYQKCA TAGCHDNMDK KDKSAKGYYH AMHDKGTKFK SCVGCHLETA GADAAKKKEL
TGCKGSKCHS
