RUBR_DESVM
ID RUBR_DESVM Reviewed; 52 AA.
AC P15412; B8DMY0;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1990, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Rubredoxin;
DE Short=Rd;
GN Name=rub; OrderedLocusNames=DvMF_2480;
OS Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Desulfovibrio.
OX NCBI_TaxID=883;
RN [1]
RP PROTEIN SEQUENCE, AND FORMYLATION AT MET-1.
RX PubMed=2561345; DOI=10.1016/0300-9084(89)90020-5;
RA Shimuzu F., Ogata M., Yagi T., Wakabayashi S., Matsubara H.;
RT "Amino acid sequence and function of rubredoxin from Desulfovibrio vulgaris
RT Miyazaki.";
RL Biochimie 71:1171-1177(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9116039; DOI=10.1016/s0167-4781(96)00203-5;
RA Kitamura M., Koshino Y., Kamikawa Y., Kohno K., Kojima S., Miura K.,
RA Sagara T., Akutsu H., Kumagai I., Nakaya T.;
RT "Cloning and expression of the rubredoxin gene from Desulfovibrio vulgaris
RT (Miyazaki F) -- comparison of the primary structure of desulfoferrodoxin.";
RL Biochim. Biophys. Acta 1351:239-247(1997).
RN [3]
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 [4]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RC STRAIN=IAM 12604;
RX PubMed=10089348; DOI=10.1107/s0907444998011810;
RA Misaki S., Morimoto Y., Ogata M., Yagi T., Higuchi Y., Yasuoka N.;
RT "Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki
RT F in two crystal forms.";
RL Acta Crystallogr. D 55:408-413(1999).
CC -!- FUNCTION: Rubredoxin is a small nonheme, iron protein lacking acid-
CC labile sulfide. Its single Fe, chelated to 4 Cys, functions as an
CC electron acceptor and may also stabilize the conformation of the
CC molecule.
CC -!- FUNCTION: Electron acceptor for cytoplasmic lactate dehydrogenase.
CC -!- COFACTOR:
CC Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
CC Note=Binds 1 Fe(3+) ion per subunit.;
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the rubredoxin family. {ECO:0000305}.
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DR EMBL; D76419; BAA11175.1; -; Genomic_DNA.
DR EMBL; CP001197; ACL09420.1; -; Genomic_DNA.
DR PIR; JX0241; JX0241.
DR RefSeq; WP_007526280.1; NC_011769.1.
DR PDB; 1RDV; X-ray; 2.00 A; A=1-52.
DR PDB; 2RDV; X-ray; 1.90 A; A/B/C=1-52.
DR PDBsum; 1RDV; -.
DR PDBsum; 2RDV; -.
DR AlphaFoldDB; P15412; -.
DR SMR; P15412; -.
DR STRING; 883.DvMF_2480; -.
DR EnsemblBacteria; ACL09420; ACL09420; DvMF_2480.
DR KEGG; dvm:DvMF_2480; -.
DR eggNOG; COG1773; Bacteria.
DR HOGENOM; CLU_128747_3_3_7; -.
DR OMA; APKDMFE; -.
DR OrthoDB; 2047418at2; -.
DR EvolutionaryTrace; P15412; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR CDD; cd00730; rubredoxin; 1.
DR InterPro; IPR024922; Rubredoxin.
DR InterPro; IPR024934; Rubredoxin-like_dom.
DR InterPro; IPR024935; Rubredoxin_dom.
DR InterPro; IPR018527; Rubredoxin_Fe_BS.
DR Pfam; PF00301; Rubredoxin; 1.
DR PIRSF; PIRSF000071; Rubredoxin; 1.
DR PRINTS; PR00163; RUBREDOXIN.
DR PROSITE; PS00202; RUBREDOXIN; 1.
DR PROSITE; PS50903; RUBREDOXIN_LIKE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Electron transport;
KW Formylation; Iron; Metal-binding; Transport.
FT CHAIN 1..52
FT /note="Rubredoxin"
FT /id="PRO_0000135039"
FT DOMAIN 1..52
FT /note="Rubredoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00241"
FT BINDING 6
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 9
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 39
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 42
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT MOD_RES 1
FT /note="N-formylmethionine"
FT /evidence="ECO:0000269|PubMed:2561345"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:2RDV"
FT TURN 7..9
FT /evidence="ECO:0007829|PDB:2RDV"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:2RDV"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:2RDV"
FT HELIX 30..32
FT /evidence="ECO:0007829|PDB:2RDV"
FT TURN 40..42
FT /evidence="ECO:0007829|PDB:2RDV"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:2RDV"
FT STRAND 49..51
FT /evidence="ECO:0007829|PDB:2RDV"
SQ SEQUENCE 52 AA; 5598 MW; 6443741A8A8063A2 CRC64;
MKKYVCTVCG YEYDPAEGDP DNGVKPGTAF EDVPADWVCP ICGAPKSEFE PA
