DFX_DESDA
ID DFX_DESDA Reviewed; 126 AA.
AC P22076; B8J2Y7;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 3.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Desulfoferrodoxin;
DE Short=Dfx;
DE EC=1.15.1.2;
DE AltName: Full=Superoxide reductase;
DE Short=SOR;
GN Name=dfx; OrderedLocusNames=Ddes_2010;
OS Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Desulfovibrio.
OX NCBI_TaxID=525146;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27774 / DSM 6949 / MB;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D.,
RA Goodwin L., Pitluck S., Sims D., Lu M., Kiss H., Meineke L., Brettin T.,
RA Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Ovchinnikova G., Hazen T.C.;
RT "Complete sequence of Desulfovibrio desulfuricans subsp. desulfuricans str.
RT ATCC 27774.";
RL Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP PROTEIN SEQUENCE OF 2-126, AND MASS SPECTROMETRY.
RX PubMed=8647238; DOI=10.1016/0014-5793(96)00364-x;
RA Devreese B., Tavares P., Lampreia J., Van Damme N., Le Gall J.,
RA Moura J.J.G., Van Beeumen J., Moura I.;
RT "Primary structure of desulfoferrodoxin from Desulfovibrio desulfuricans
RT ATCC 27774, a new class of non-heme iron proteins.";
RL FEBS Lett. 385:138-142(1996).
RN [3]
RP PROTEIN SEQUENCE OF 2-45, AND SPECTROSCOPIC STUDIES.
RX PubMed=2174880; DOI=10.1016/s0021-9258(18)45782-1;
RA Moura I., Tavares P., Moura J.J.G., Ravi N., Huynh B.H., Liu M.-Y.,
RA Le Gall J.;
RT "Purification and characterization of desulfoferrodoxin. A novel protein
RT from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio
RT vulgaris (strain Hildenborough) that contains a distorted rubredoxin center
RT and a mononuclear ferrous center.";
RL J. Biol. Chem. 265:21596-21602(1990).
RN [4]
RP COFACTOR, REDOX POTENTIAL, AND SPECTROSCOPIC STUDIES.
RX PubMed=8144635; DOI=10.1016/s0021-9258(17)34088-7;
RA Tavares P., Ravi N., Moura J.J.G., Le Gall J., Huang Y.-H., Crouse B.R.,
RA Johnson M.K., Huynh B.H., Moura I.;
RT "Spectroscopic properties of desulfoferrodoxin from Desulfovibrio
RT desulfuricans (ATCC 27774).";
RL J. Biol. Chem. 269:10504-10510(1994).
RN [5]
RP CRYSTALLIZATION.
RX PubMed=8762151; DOI=10.1002/pro.5560050622;
RA Coelho A.V., Matias P.M., Carrondo M.A., Tavares P., Moura J.J.G.,
RA Moura I., Fuelop V., Hajdu J., Le Gall J.;
RT "Preliminary crystallographic analysis of the oxidized form of a two mono-
RT nuclear iron centres protein from Desulfovibrio desulfuricans ATCC 27774.";
RL Protein Sci. 5:1189-1191(1996).
RN [6]
RP PRELIMINARY FUNCTION.
RX PubMed=10215854; DOI=10.1046/j.1432-1327.1999.00278.x;
RA Romao C.V., Liu M.-Y., Le Gall J., Gomes C.M., Braga V., Pacheco I.,
RA Xavier A.V., Teixeira M.;
RT "The superoxide dismutase activity of desulfoferrodoxin from Desulfovibrio
RT desulfuricans ATCC 27774.";
RL Eur. J. Biochem. 261:438-443(1999).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), COFACTOR, AND SUBUNIT.
RA Coelho A.V., Matias P.M., Fueloep V., Thompson A., Gonzalez A.,
RA Carrondo M.A.;
RT "Desulfoferrodoxin structure determined by MAD phasing and refinement to
RT 1.9-A resolution reveals a unique combination of a tetrahedral FeS4 centre
RT with a square pyramidal FeSN4 centre.";
RL J. Biol. Inorg. Chem. 2:680-689(1997).
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 (By similarity). {ECO:0000250}.
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:0000250|UniProtKB:Q97GB9};
CC -!- COFACTOR:
CC Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
CC Note=Binds 1 Fe(3+) ion per subunit. The iron ion 1 is coordinated via
CC 4 cysteine residues.;
CC -!- COFACTOR:
CC Name=Cu(2+); Xref=ChEBI:CHEBI:29036;
CC Note=Binds 1 Fe(2+) ion per subunit. The iron ion 2 is coordinated via
CC four histidines and one cysteine residue.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Redox potential:
CC E(0) is +4 mV for center I and +240 mV for center II.;
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.7}.
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=13881.3; Mass_error=0.1; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:8647238};
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 (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the desulfoferrodoxin family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a superoxide dismutase.
CC {ECO:0000305|PubMed:10215854}.
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DR EMBL; CP001358; ACL49906.1; -; Genomic_DNA.
DR PIR; S68837; S68837.
DR RefSeq; WP_012625630.1; NC_011883.1.
DR PDB; 1DFX; X-ray; 1.90 A; A=2-126.
DR PDBsum; 1DFX; -.
DR AlphaFoldDB; P22076; -.
DR SMR; P22076; -.
DR STRING; 525146.Ddes_2010; -.
DR EnsemblBacteria; ACL49906; ACL49906; Ddes_2010.
DR KEGG; dds:Ddes_2010; -.
DR eggNOG; COG2033; Bacteria.
DR HOGENOM; CLU_118960_1_0_7; -.
DR OMA; EEKHYIQ; -.
DR OrthoDB; 1496450at2; -.
DR BRENDA; 1.15.1.2; 1905.
DR EvolutionaryTrace; P22076; -.
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; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2174880,
FT ECO:0000269|PubMed:8647238"
FT CHAIN 2..126
FT /note="Desulfoferrodoxin"
FT /id="PRO_0000140864"
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 CONFLICT 44..45
FT /note="GA -> DH (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:1DFX"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:1DFX"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:1DFX"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 77..84
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:1DFX"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:1DFX"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:1DFX"
SQ SEQUENCE 126 AA; 14013 MW; 5B827A5A7D9EF1A3 CRC64;
MPKHLEVYKC THCGNIVEVL HGGGAELVCC GEPMKHMVEG STDGAMEKHV PVIEKVDGGY
LIKVGSVPHP MEEKHWIEWI ELLADGRSYT KFLKPGDAPE AFFAIDASKV TAREYCNLHG
HWKAEN
