DFX_DESB2
ID DFX_DESB2 Reviewed; 126 AA.
AC Q46495; E1QI98;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Desulfoferrodoxin;
DE Short=Dfx;
DE EC=1.15.1.2;
DE AltName: Full=Superoxide reductase;
DE Short=SOR;
GN Name=dfx; Synonyms=rbo; OrderedLocusNames=Deba_2050;
OS Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802
OS / 2st14).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfarculales;
OC Desulfarculaceae; Desulfarculus.
OX NCBI_TaxID=644282;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14;
RX PubMed=8955290; DOI=10.1128/jb.178.23.6736-6742.1996;
RA Pianzzola M.J., Soubes M., Touati D.;
RT "Overproduction of the rbo gene product from Desulfovibrio species
RT suppresses all deleterious effects of lack of superoxide dismutase in
RT Escherichia coli.";
RL J. Bacteriol. 178:6736-6742(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14;
RX PubMed=21304732; DOI=10.4056/sigs.1243258;
RA Sun H., Spring S., Lapidus A., Davenport K., Del Rio T.G., Tice H.,
RA Nolan M., Copeland A., Cheng J.F., Lucas S., Tapia R., Goodwin L.,
RA Pitluck S., Ivanova N., Pagani I., Mavromatis K., Ovchinnikova G., Pati A.,
RA Chen A., Palaniappan K., Hauser L., Chang Y.J., Jeffries C.D., Detter J.C.,
RA Han C., Rohde M., Brambilla E., Goker M., Woyke T., Bristow J., Eisen J.A.,
RA Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Land M.;
RT "Complete genome sequence of Desulfarculus baarsii type strain (2st14).";
RL Stand. Genomic Sci. 3:276-284(2010).
RN [3]
RP PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MASS
RP SPECTROMETRY, ABSORPTION SPECTROSCOPY, EPR SPECTROSCOPY, AND KINETIC
RP STUDIES.
RX PubMed=10617593; DOI=10.1074/jbc.275.1.115;
RA Lombard M., Fontecave M., Touati D., Niviere V.;
RT "Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with
RT superoxide anion. Evidence for a superoxide reductase activity.";
RL J. Biol. Chem. 275:115-121(2000).
RN [4]
RP MUTAGENESIS OF GLU-47 AND LYS-48.
RX PubMed=11305919; DOI=10.1021/bi0023908;
RA Lombard M., Houee-Levin C., Touati D., Fontecave M., Niviere V.;
RT "Superoxide reductase from Desulfoarculus baarsii: reaction mechanism and
RT role of glutamate 47 and lysine 48 in catalysis.";
RL Biochemistry 40:5032-5040(2001).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.15 ANGSTROMS) OF MUTANT ALA-47 UNCOMPLEXED AND IN
RP COMPLEX WITH FERROCYANIDE, COFACTOR, AND SUBUNIT.
RX PubMed=15341736; DOI=10.1016/j.str.2004.07.013;
RA Adam V., Royant A., Niviere V., Molina-Heredia F.P., Bourgeois D.;
RT "Structure of superoxide reductase bound to ferrocyanide and active site
RT expansion upon X-ray-induced photo-reduction.";
RL Structure 12:1729-1740(2004).
CC -!- FUNCTION: Catalyzes the one-electron reduction of superoxide anion
CC radical to hydrogen peroxide at a nonheme ferrous iron center. Plays a
CC fundamental role in case of oxidative stress via its superoxide
CC detoxification activity. {ECO:0000269|PubMed:10617593}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 H(+) + reduced [rubredoxin] + superoxide = H2O2 + oxidized
CC [rubredoxin]; Xref=Rhea:RHEA:21324, Rhea:RHEA-COMP:10302, Rhea:RHEA-
CC COMP:10303, ChEBI:CHEBI:15378, ChEBI:CHEBI:16240, ChEBI:CHEBI:18421,
CC ChEBI:CHEBI:29033, ChEBI:CHEBI:29034; EC=1.15.1.2;
CC Evidence={ECO:0000269|PubMed:10617593};
CC -!- COFACTOR:
CC Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
CC Evidence={ECO:0000269|PubMed:15341736};
CC Note=Binds 1 Fe(3+) ion per subunit. The iron ion 1 is coordinated via
CC 4 cysteine residues. {ECO:0000269|PubMed:15341736};
CC -!- COFACTOR:
CC Name=Cu(2+); Xref=ChEBI:CHEBI:29036;
CC Evidence={ECO:0000269|PubMed:15341736};
CC Note=Binds 1 Fe(2+) ion per subunit. The iron ion 2 is coordinated via
CC four histidines and one cysteine residue.
CC {ECO:0000269|PubMed:15341736};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10617593,
CC ECO:0000269|PubMed:15341736}.
CC -!- DOMAIN: Is organized in two protein domains. The N-terminal domain has
CC a fold similar to that of desulforedoxin and contains a mononuclear
CC Fe(3+) ion, center I. The second domain contains a different
CC mononuclear iron center, center II, with a Fe(2+) ion.
CC -!- MASS SPECTROMETRY: Mass=14028; Mass_error=2; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:10617593};
CC -!- MISCELLANEOUS: Catalysis occurs at center II. Fe(2+) ion of center II
CC is the electron donor and is converted to the Fe(3+) form during the
CC reaction.
CC -!- MISCELLANEOUS: The protein sequence in PubMed:10617593 comes from
CC protein overexpressed and processed in E.coli.
CC -!- SIMILARITY: Belongs to the desulfoferrodoxin family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a rubredoxin oxidoreductase.
CC {ECO:0000305|PubMed:8955290}.
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DR EMBL; X99543; CAA67880.1; -; Genomic_DNA.
DR EMBL; CP002085; ADK85415.1; -; Genomic_DNA.
DR RefSeq; WP_013258856.1; NC_014365.1.
DR PDB; 1VZG; X-ray; 1.69 A; A/B=1-126.
DR PDB; 1VZH; X-ray; 1.69 A; A/B=1-126.
DR PDB; 1VZI; X-ray; 1.15 A; A/B=1-126.
DR PDB; 2JI1; X-ray; 1.70 A; A/B/C/D=2-126.
DR PDB; 2JI2; X-ray; 1.70 A; A/B/C/D=2-126.
DR PDB; 2JI3; X-ray; 1.95 A; A/B/C/D=2-126.
DR PDBsum; 1VZG; -.
DR PDBsum; 1VZH; -.
DR PDBsum; 1VZI; -.
DR PDBsum; 2JI1; -.
DR PDBsum; 2JI2; -.
DR PDBsum; 2JI3; -.
DR AlphaFoldDB; Q46495; -.
DR SMR; Q46495; -.
DR STRING; 644282.Deba_2050; -.
DR EnsemblBacteria; ADK85415; ADK85415; Deba_2050.
DR KEGG; dbr:Deba_2050; -.
DR eggNOG; COG2033; Bacteria.
DR HOGENOM; CLU_118960_1_0_7; -.
DR OMA; EEKHYIQ; -.
DR OrthoDB; 1496450at2; -.
DR BRENDA; 1.15.1.2; 1883.
DR EvolutionaryTrace; Q46495; -.
DR Proteomes; UP000009047; Chromosome.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0050605; F:superoxide reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0019430; P:removal of superoxide radicals; IEA:InterPro.
DR CDD; cd00974; DSRD; 1.
DR Gene3D; 2.20.28.100; -; 1.
DR Gene3D; 2.60.40.730; -; 1.
DR InterPro; IPR002742; Desulfoferrodoxin_Fe-bd_dom.
DR InterPro; IPR036073; Desulfoferrodoxin_Fe-bd_dom_sf.
DR InterPro; IPR004462; Desulfoferrodoxin_N.
DR InterPro; IPR038094; Desulfoferrodoxin_N_sf.
DR InterPro; IPR004793; Desulfoferrodoxin_rbo.
DR Pfam; PF06397; Desulfoferrod_N; 1.
DR Pfam; PF01880; Desulfoferrodox; 1.
DR SUPFAM; SSF49367; SSF49367; 1.
DR TIGRFAMs; TIGR00319; desulf_FeS4; 1.
DR TIGRFAMs; TIGR00320; dfx_rbo; 1.
DR TIGRFAMs; TIGR00332; neela_ferrous; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Detoxification; Direct protein sequencing;
KW Electron transport; Iron; Metal-binding; Oxidoreductase;
KW Reference proteome; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10617593"
FT CHAIN 2..126
FT /note="Desulfoferrodoxin"
FT /id="PRO_0000140863"
FT BINDING 10
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 13
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 29
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 30
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 49
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 69
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 75
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 116
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 119
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT MUTAGEN 47
FT /note="E->A: No effect."
FT /evidence="ECO:0000269|PubMed:11305919"
FT MUTAGEN 48
FT /note="K->I: Decrease in reaction rate."
FT /evidence="ECO:0000269|PubMed:11305919"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:1VZI"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 16..21
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:1VZI"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:1VZI"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 73..75
FT /evidence="ECO:0007829|PDB:2JI3"
FT STRAND 77..84
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:1VZI"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:1VZI"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:1VZI"
SQ SEQUENCE 126 AA; 14157 MW; 558719E66B7FA5EC CRC64;
MPERLQVYKC EVCGNIVEVL NGGIGELVCC NQDMKLMSEN TVDAAKEKHV PVIEKIDGGY
KVKVGAVAHP MEEKHYIQWI ELLADDKCYT QFLKPGQAPE AVFLIEAAKV VAREYCNIHG
HWKAEN
