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Protein

Desulfoferrodoxin

Gene

dfx

Organism
Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the one-electron reduction of superoxide anion radical to hydrogen peroxide at a nonheme ferrous iron center. Plays a fundamental role in case of oxidative stress via its superoxide detoxification activity.1 Publication

Catalytic activityi

Reduced rubredoxin + superoxide + 2 H+ = oxidized rubredoxin + H2O2.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Fe3+1 PublicationNote: Binds 1 Fe3+ ion per subunit. The iron ion 1 is coordinated via 4 cysteine residues.1 Publication
  • Cu2+1 PublicationNote: Binds 1 Fe2+ ion per subunit. The iron ion 2 is coordinated via four histidines and one cysteine residue.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi10 – 101Iron 1
Metal bindingi13 – 131Iron 1
Metal bindingi29 – 291Iron 1
Metal bindingi30 – 301Iron 1
Metal bindingi49 – 491Iron 2; catalytic
Metal bindingi69 – 691Iron 2; catalytic
Metal bindingi75 – 751Iron 2; catalytic
Metal bindingi116 – 1161Iron 2; catalytic
Metal bindingi119 – 1191Iron 2; catalytic

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Detoxification, Electron transport, Transport

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciDBAA644282:GH2J-2085-MONOMER.
BRENDAi1.15.1.2. 1883.

Names & Taxonomyi

Protein namesi
Recommended name:
Desulfoferrodoxin (EC:1.15.1.2)
Short name:
Dfx
Alternative name(s):
Superoxide reductase
Short name:
SOR
Gene namesi
Name:dfx
Synonyms:rbo
Ordered Locus Names:Deba_2050
OrganismiDesulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14)
Taxonomic identifieri644282 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfarculalesDesulfarculaceaeDesulfarculus
Proteomesi
  • UP000009047 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi47 – 471E → A: No effect. 1 Publication
Mutagenesisi48 – 481K → I: Decrease in reaction rate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 126125DesulfoferrodoxinPRO_0000140863Add
BLAST

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi644282.Deba_2050.

Structurei

Secondary structure

1
126
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 93Combined sources
Turni11 – 133Combined sources
Beta strandi16 – 216Combined sources
Beta strandi27 – 293Combined sources
Beta strandi42 – 443Combined sources
Helixi46 – 494Combined sources
Beta strandi50 – 567Combined sources
Beta strandi59 – 646Combined sources
Turni65 – 684Combined sources
Beta strandi73 – 753Combined sources
Beta strandi77 – 848Combined sources
Beta strandi87 – 926Combined sources
Beta strandi99 – 1046Combined sources
Beta strandi111 – 1166Combined sources
Turni117 – 1193Combined sources
Beta strandi120 – 1256Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VZGX-ray1.69A/B1-126[»]
1VZHX-ray1.69A/B1-126[»]
1VZIX-ray1.15A/B1-126[»]
2JI1X-ray1.70A/B/C/D2-126[»]
2JI2X-ray1.70A/B/C/D2-126[»]
2JI3X-ray1.95A/B/C/D2-126[»]
ProteinModelPortaliQ46495.
SMRiQ46495. Positions 2-126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46495.

Family & Domainsi

Domaini

Is organized in two protein domains. The N-terminal domain has a fold similar to that of desulforedoxin and contains a mononuclear Fe3+ ion, center I. The second domain contains a different mononuclear iron center, center II, with a Fe2+ ion.

Sequence similaritiesi

Belongs to the desulfoferrodoxin family.Curated

Phylogenomic databases

eggNOGiENOG4105MAX. Bacteria.
COG2033. LUCA.
HOGENOMiHOG000008863.
KOiK05919.
OMAiAGELVCC.

Family and domain databases

InterProiIPR002742. Desulfoferrodoxin_Fe-bd_dom.
IPR004462. Desulfoferrodoxin_FeS4.
IPR004793. Desulfoferrodoxin_rbo.
[Graphical view]
PfamiPF06397. Desulfoferrod_N. 1 hit.
PF01880. Desulfoferrodox. 1 hit.
[Graphical view]
SUPFAMiSSF49367. SSF49367. 1 hit.
TIGRFAMsiTIGR00319. desulf_FeS4. 1 hit.
TIGR00320. dfx_rbo. 1 hit.
TIGR00332. neela_ferrous. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q46495-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPERLQVYKC EVCGNIVEVL NGGIGELVCC NQDMKLMSEN TVDAAKEKHV
60 70 80 90 100
PVIEKIDGGY KVKVGAVAHP MEEKHYIQWI ELLADDKCYT QFLKPGQAPE
110 120
AVFLIEAAKV VAREYCNIHG HWKAEN
Length:126
Mass (Da):14,157
Last modified:January 23, 2007 - v3
Checksum:i558719E66B7FA5EC
GO

Mass spectrometryi

Molecular mass is 14028±2 Da from positions 2 - 126. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99543 Genomic DNA. Translation: CAA67880.1.
CP002085 Genomic DNA. Translation: ADK85415.1.
RefSeqiWP_013258856.1. NC_014365.1.

Genome annotation databases

EnsemblBacteriaiADK85415; ADK85415; Deba_2050.
KEGGidbr:Deba_2050.
PATRICi42299615. VBIDesBaa100999_2101.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99543 Genomic DNA. Translation: CAA67880.1.
CP002085 Genomic DNA. Translation: ADK85415.1.
RefSeqiWP_013258856.1. NC_014365.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VZGX-ray1.69A/B1-126[»]
1VZHX-ray1.69A/B1-126[»]
1VZIX-ray1.15A/B1-126[»]
2JI1X-ray1.70A/B/C/D2-126[»]
2JI2X-ray1.70A/B/C/D2-126[»]
2JI3X-ray1.95A/B/C/D2-126[»]
ProteinModelPortaliQ46495.
SMRiQ46495. Positions 2-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi644282.Deba_2050.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADK85415; ADK85415; Deba_2050.
KEGGidbr:Deba_2050.
PATRICi42299615. VBIDesBaa100999_2101.

Phylogenomic databases

eggNOGiENOG4105MAX. Bacteria.
COG2033. LUCA.
HOGENOMiHOG000008863.
KOiK05919.
OMAiAGELVCC.

Enzyme and pathway databases

BioCyciDBAA644282:GH2J-2085-MONOMER.
BRENDAi1.15.1.2. 1883.

Miscellaneous databases

EvolutionaryTraceiQ46495.

Family and domain databases

InterProiIPR002742. Desulfoferrodoxin_Fe-bd_dom.
IPR004462. Desulfoferrodoxin_FeS4.
IPR004793. Desulfoferrodoxin_rbo.
[Graphical view]
PfamiPF06397. Desulfoferrod_N. 1 hit.
PF01880. Desulfoferrodox. 1 hit.
[Graphical view]
SUPFAMiSSF49367. SSF49367. 1 hit.
TIGRFAMsiTIGR00319. desulf_FeS4. 1 hit.
TIGR00320. dfx_rbo. 1 hit.
TIGR00332. neela_ferrous. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Overproduction of the rbo gene product from Desulfovibrio species suppresses all deleterious effects of lack of superoxide dismutase in Escherichia coli."
    Pianzzola M.J., Soubes M., Touati D.
    J. Bacteriol. 178:6736-6742(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14.
  3. "Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with superoxide anion. Evidence for a superoxide reductase activity."
    Lombard M., Fontecave M., Touati D., Niviere V.
    J. Biol. Chem. 275:115-121(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MASS SPECTROMETRY, ABSORPTION SPECTROSCOPY, EPR SPECTROSCOPY, KINETIC STUDIES.
  4. "Superoxide reductase from Desulfoarculus baarsii: reaction mechanism and role of glutamate 47 and lysine 48 in catalysis."
    Lombard M., Houee-Levin C., Touati D., Fontecave M., Niviere V.
    Biochemistry 40:5032-5040(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-47 AND LYS-48.
  5. "Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction."
    Adam V., Royant A., Niviere V., Molina-Heredia F.P., Bourgeois D.
    Structure 12:1729-1740(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.15 ANGSTROMS) OF MUTANT ALA-47 UNCOMPLEXED AND IN COMPLEX WITH FERROCYANIDE, COFACTOR, SUBUNIT.

Entry informationi

Entry nameiDFX_DESB2
AccessioniPrimary (citable) accession number: Q46495
Secondary accession number(s): E1QI98
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 23, 2007
Last modified: November 11, 2015
This is version 110 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Catalysis occurs at center II. Fe2+ ion of center II is the electron donor and is converted to the Fe3+ form during the reaction.
The protein sequence in PubMed:10617593 comes from protein overexpressed and processed in E.coli.

Caution

Was originally thought to be a rubredoxin oxidoreductase.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.