RUBY_DESVH
ID RUBY_DESVH Reviewed; 191 AA.
AC P24931;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-1992, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Rubrerythrin;
DE Short=Rr;
GN Name=rbr; OrderedLocusNames=DVU_3094;
OS Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM
OS B-1760 / Hildenborough).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Desulfovibrio.
OX NCBI_TaxID=882;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1932032; DOI=10.1021/bi00110a014;
RA Prickril B.C., Kurtz D.M. Jr., LeGall J., Voordouw G.;
RT "Cloning and sequencing of the gene for rubrerythrin from Desulfovibrio
RT vulgaris (Hildenborough).";
RL Biochemistry 30:11118-11123(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Lumppio H.L., Shenvi N.V., Garg R.P., Summers A.O., Kurtz D.M. Jr.;
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROTEIN SEQUENCE.
RX PubMed=1657933; DOI=10.1016/s0021-9258(18)54757-8;
RA van Beeumen J.J., van Driessche G., Liu M.-Y., LeGall J.;
RT "The primary structure of rubrerythrin, a protein with inorganic
RT pyrophosphatase activity from Desulfovibrio vulgaris. Comparison with
RT hemerythrin and rubredoxin.";
RL J. Biol. Chem. 266:20645-20653(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough;
RX PubMed=15077118; DOI=10.1038/nbt959;
RA Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T.,
RA Kolonay J.F., Eisen J.A., Ward N.L., Methe B.A., Brinkac L.M.,
RA Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R.,
RA Nelson W.C., Sullivan S.A., Fouts D.E., Haft D.H., Selengut J.,
RA Peterson J.D., Davidsen T.M., Zafar N., Zhou L., Radune D., Dimitrov G.,
RA Hance M., Tran K., Khouri H.M., Gill J., Utterback T.R., Feldblyum T.V.,
RA Wall J.D., Voordouw G., Fraser C.M.;
RT "The genome sequence of the anaerobic, sulfate-reducing bacterium
RT Desulfovibrio vulgaris Hildenborough.";
RL Nat. Biotechnol. 22:554-559(2004).
RN [5]
RP PROTEIN SEQUENCE OF 1-15, AND CHARACTERIZATION OF IRON-BINDING SITES.
RX PubMed=8383040; DOI=10.1111/j.1432-1033.1993.tb17655.x;
RA Pierik A.J., Wolbert R.B.G., Portier G.L., Verhagen M.F.J.M., Hagen W.R.;
RT "Nigerythrin and rubrerythrin from Desulfovibrio vulgaris each contain two
RT mononuclear iron centers and two dinuclear iron clusters.";
RL Eur. J. Biochem. 212:237-245(1993).
RN [6]
RP POSSIBLE BINUCLEAR IRON-SITES.
RX PubMed=1958203; DOI=10.1016/s0006-291x(05)81423-8;
RA Kurtz D.M. Jr., Prickril B.C.;
RT "Intrapeptide sequence homology in rubrerythrin from Desulfovibrio
RT vulgaris: identification of potential ligands to the diiron site.";
RL Biochem. Biophys. Res. Commun. 181:337-341(1991).
RN [7]
RP CHARACTERIZATION.
RX PubMed=2835096; DOI=10.1021/bi00405a037;
RA LeGall J., Prickril B.C., Moura I., Xavier A.V., Moura J.J.G., Huynh B.H.;
RT "Isolation and characterization of rubrerythrin, a non-heme iron protein
RT from Desulfovibrio vulgaris that contains rubredoxin centers and a
RT hemerythrin-like binuclear iron cluster.";
RL Biochemistry 27:1636-1642(1988).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX PubMed=8646540; DOI=10.1038/nsb0696-539;
RA deMare F., Kurtz D.M. Jr., Nordlund P.;
RT "The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique
RT combination of rubredoxin-like FeS4 and ferritin-like diiron domains.";
RL Nat. Struct. Biol. 3:539-546(1996).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX PubMed=10201393; DOI=10.1038/7538;
RA Sieker L.C., Holmes M., Le Trong I., Turley S., Santarsiero B.D.,
RA Liu M.-Y., LeGall J., Stenkamp R.E.;
RT "Alternative metal-binding sites in rubrerythrin.";
RL Nat. Struct. Biol. 6:308-309(1999).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX PubMed=10968622; DOI=10.1007/pl00021450;
RA Sieker L.C., Holmes M., Le Trong I., Turley S., Liu M.-Y., LeGall J.,
RA Stenkamp R.E.;
RT "The 1.9 A crystal structure of the 'as isolated' rubrerythrin from
RT Desulfovibrio vulgaris: some surprising results.";
RL J. Biol. Inorg. Chem. 5:505-513(2000).
RN [11] {ECO:0007744|PDB:1LKM, ECO:0007744|PDB:1LKO, ECO:0007744|PDB:1LKP}
RP X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) IN COMPLEX WITH IRON IONS.
RX PubMed=12175244; DOI=10.1021/ja026587u;
RA Jin S., Kurtz D.M. Jr., Liu Z.-J., Rose J., Wang B.-C.;
RT "X-ray crystal structures of reduced rubrerythrin and its azide adduct: a
RT structure-based mechanism for a non-heme diiron peroxidase.";
RL J. Am. Chem. Soc. 124:9845-9855(2002).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=12459910; DOI=10.1007/s00775-002-0400-0;
RA Li M., Liu M.-Y., LeGall J., Gui L.-L., Liao J., Jiang T., Zhang J.-P.,
RA Liang D.-C., Chang W.-R.;
RT "Crystal structure studies on rubrerythrin: enzymatic activity in relation
RT to the zinc movement.";
RL J. Biol. Inorg. Chem. 8:149-155(2003).
CC -!- FUNCTION: May provide oxidative stress protection via catalytic
CC reduction of intracellular hydrogen peroxide. {ECO:0000250}.
CC -!- COFACTOR:
CC Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
CC Note=Binds 3 Fe(3+) ions per subunit.;
CC -!- SUBUNIT: Homodimer. Possesses two rubredoxin-like centers and two non-
CC sulfur oxo-bridged di-iron centers per dimer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- CAUTION: Was originally thought to have inorganic pyrophosphatase
CC activity. {ECO:0000305}.
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DR EMBL; U82323; AAB39991.1; -; Genomic_DNA.
DR EMBL; AE017285; AAS97565.1; -; Genomic_DNA.
DR PIR; A41191; A39492.
DR RefSeq; WP_010940353.1; NZ_CABHLV010000001.1.
DR RefSeq; YP_012305.1; NC_002937.3.
DR PDB; 1B71; X-ray; 1.90 A; A=1-191.
DR PDB; 1DVB; X-ray; 1.90 A; A=1-191.
DR PDB; 1JYB; X-ray; 2.20 A; A=1-191.
DR PDB; 1LKM; X-ray; 1.69 A; A=1-191.
DR PDB; 1LKO; X-ray; 1.63 A; A=1-191.
DR PDB; 1LKP; X-ray; 1.64 A; A=1-191.
DR PDB; 1QYB; X-ray; 1.75 A; A=1-191.
DR PDB; 1RYT; X-ray; 2.10 A; A=2-191.
DR PDB; 1S2Z; X-ray; 1.75 A; A=1-191.
DR PDB; 1S30; X-ray; 2.05 A; A=1-191.
DR PDBsum; 1B71; -.
DR PDBsum; 1DVB; -.
DR PDBsum; 1JYB; -.
DR PDBsum; 1LKM; -.
DR PDBsum; 1LKO; -.
DR PDBsum; 1LKP; -.
DR PDBsum; 1QYB; -.
DR PDBsum; 1RYT; -.
DR PDBsum; 1S2Z; -.
DR PDBsum; 1S30; -.
DR AlphaFoldDB; P24931; -.
DR SMR; P24931; -.
DR STRING; 882.DVU_3094; -.
DR PaxDb; P24931; -.
DR PRIDE; P24931; -.
DR EnsemblBacteria; AAS97565; AAS97565; DVU_3094.
DR KEGG; dvu:DVU_3094; -.
DR PATRIC; fig|882.5.peg.2807; -.
DR eggNOG; COG1592; Bacteria.
DR HOGENOM; CLU_095256_0_1_7; -.
DR OMA; PQAYFEV; -.
DR PhylomeDB; P24931; -.
DR EvolutionaryTrace; P24931; -.
DR Proteomes; UP000002194; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005506; F:iron ion binding; IDA:UniProtKB.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR CDD; cd01041; Rubrerythrin; 1.
DR Gene3D; 1.20.1260.10; -; 1.
DR InterPro; IPR012347; Ferritin-like.
DR InterPro; IPR009040; Ferritin-like_diiron.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR024934; Rubredoxin-like_dom.
DR InterPro; IPR003251; Rubrerythrin.
DR Pfam; PF02915; Rubrerythrin; 1.
DR SUPFAM; SSF47240; SSF47240; 1.
DR PROSITE; PS50905; FERRITIN_LIKE; 1.
DR PROSITE; PS50903; RUBREDOXIN_LIKE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Electron transport;
KW Iron; Metal-binding; Reference proteome; Transport; Zinc.
FT CHAIN 1..191
FT /note="Rubrerythrin"
FT /id="PRO_0000135064"
FT DOMAIN 1..146
FT /note="Ferritin-like diiron"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00085"
FT DOMAIN 153..191
FT /note="Rubredoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00241"
FT BINDING 20
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 53
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 53
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 94
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 97
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 128
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 128
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 131
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 158
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 161
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 174
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT BINDING 177
FT /ligand="Fe(3+)"
FT /ligand_id="ChEBI:CHEBI:29034"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12175244,
FT ECO:0007744|PDB:1LKM"
FT STRAND 5..7
FT /evidence="ECO:0007829|PDB:1RYT"
FT HELIX 8..36
FT /evidence="ECO:0007829|PDB:1LKO"
FT HELIX 40..63
FT /evidence="ECO:0007829|PDB:1LKO"
FT HELIX 83..99
FT /evidence="ECO:0007829|PDB:1LKO"
FT HELIX 101..112
FT /evidence="ECO:0007829|PDB:1LKO"
FT HELIX 115..143
FT /evidence="ECO:0007829|PDB:1LKO"
FT STRAND 147..158
FT /evidence="ECO:0007829|PDB:1LKO"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:1LKO"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:1LKO"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:1LKO"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:1LKO"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:1LKO"
SQ SEQUENCE 191 AA; 21544 MW; BCF8E9A2659F1138 CRC64;
MKSLKGSRTE KNILTAFAGE SQARNRYNYF GGQAKKDGFV QISDIFAETA DQEREHAKRL
FKFLEGGDLE IVAAFPAGII ADTHANLIAS AAGEHHEYTE MYPSFARIAR EEGYEEIARV
FASIAVAEEF HEKRFLDFAR NIKEGRVFLR EQATKWRCRN CGYVHEGTGA PELCPACAHP
KAHFELLGIN W
