Q46495 (DFX_DESB2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Desulfoferrodoxin
Short name=Dfx
EC=1.15.1.2

Alternative name(s):
Superoxide reductase
Short name=SOR

Gene names

Name:	dfx
Synonyms:	rbo
Ordered Locus Names:	Deba_2050

Organism

Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14) [Complete proteome] [HAMAP]

Taxonomic identifier

644282 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfarculales › Desulfarculaceae › Desulfarculus

Protein attributes

Sequence length	126 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.3
Catalytic activity	Reduced rubredoxin + superoxide + 2 H+ = rubredoxin + H2O2. Ref.3
Cofactor	Binds 1 Fe3+ ion per subunit. The iron ion 1 is coordinated via 4 cysteine residues. Ref.5 Binds 1 Fe2+ ion per subunit. The iron ion 2 is coordinated via four histidines and one cysteine residue. Ref.5
Subunit structure	Homodimer. Ref.3 Ref.5
Domain	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.
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 Ref.3 comes from protein overexpressed and processed in E.coli.
Sequence similarities	Belongs to the desulfoferrodoxin family.
Caution	Was originally (Ref.1) thought to be a rubredoxin oxidoreductase.
Mass spectrometry	Molecular mass is 14028±2 Da from positions 2 - 126. Determined by ESI. Ref.3

Ontologies

Keywords
Biological process	Detoxification Electron transport Transport
Ligand	Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW removal of superoxide radicals Inferred from electronic annotation. Source: InterPro response to toxin Inferred from electronic annotation. Source: UniProtKB-KW transport Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	iron ion binding Inferred from electronic annotation. Source: InterPro superoxide reductase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 126

125

Desulfoferrodoxin

PRO_0000140863

Sites

Metal binding

10

1

Iron 1

Metal binding

13

1

Iron 1

Metal binding

29

1

Iron 1

Metal binding

30

1

Iron 1

Metal binding

49

1

Iron 2; catalytic

Metal binding

69

1

Iron 2; catalytic

Metal binding

75

1

Iron 2; catalytic

Metal binding

116

1

Iron 2; catalytic

Metal binding

119

1

Iron 2; catalytic

Experimental info

Mutagenesis

47

1

E → A: No effect. Ref.4

Mutagenesis

48

1

K → I: Decrease in reaction rate. Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

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.

.

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126

Helix Strand Turn

Details...

Beta strand

7 – 9

3

Turn

11 – 13

3

Beta strand

16 – 21

6

Beta strand

27 – 29

3

Beta strand

42 – 44

3

Helix

46 – 49

4

Beta strand

50 – 56

7

Beta strand

59 – 64

6

Turn

65 – 68

4

Beta strand

77 – 84

8

Beta strand

87 – 92

6

Beta strand

99 – 104

6

Beta strand

111 – 116

6

Turn

117 – 119

3

Beta strand

120 – 125

6

Sequences

	Sequence		Length	Mass (Da)
	Q46495 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 558719E66B7FA5EC	FASTA	126	14,157
	10 20 30 40 50 60 MPERLQVYKC EVCGNIVEVL NGGIGELVCC NQDMKLMSEN TVDAAKEKHV PVIEKIDGGY 70 80 90 100 110 120 KVKVGAVAHP MEEKHYIQWI ELLADDKCYT QFLKPGQAPE AVFLIEAAKV VAREYCNIHG HWKAEN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 8955290] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14.
[2]	"Complete genome sequence of Desulfarculus baarsii type strain (2st14)." Sun H., Spring S., Lapidus A., Davenport K., Del Rio T.G., Tice H., Nolan M., Copeland A., Cheng J.F., Lucas S., Tapia R., Goodwin L., Pitluck S., Ivanova N., Pagani I., Mavromatis K., Ovchinnikova G., Pati A. , Chen A., Palaniappan K., Hauser L., Chang Y.J., Jeffries C.D., Detter J.C., Han C., Rohde M., Brambilla E., Goker M., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Land M. Stand. Genomic Sci. 3:276-284(2010) [PubMed: 21304732] [Abstract] 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: 10617593] [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: 11305919] [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: 15341736] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.15 ANGSTROMS) OF MUTANT ALA-47 UNCOMPLEXED AND IN COMPLEX WITH FERROCYANIDE, COFACTOR, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X99543 Genomic DNA. Translation: CAA67880.1.
CP002085 Genomic DNA. Translation: ADK85415.1.

RefSeq

YP_003808009.1. NC_014365.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1VZG	X-ray	1.69	A/B	1-126	[»]
1VZH	X-ray	1.69	A/B	1-126	[»]
1VZI	X-ray	1.15	A/B	1-126	[»]
2JI1	X-ray	1.70	A/B/C/D	1-126	[»]
2JI2	X-ray	1.70	A/B/C/D	1-126	[»]
2JI3	X-ray	1.95	A/B/C/D	1-126	[»]

ProteinModelPortal

Q46495.

SMR

Q46495. Positions 2-126.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

9494519.

GenomeReviews

Gene locus Deba_2050 in contig CP002085_GR.

KEGG

dbr:Deba_2050.

PATRIC

42299615. VBIDesBaa100999_2101.

Organism-specific databases

CMR

Search...

Family and domain databases

InterPro

IPR002742. Desulfoferrodoxin_Fe-bd_dom.
IPR004462. Desulfoferrodoxin_FeS4.
IPR004793. Desulfoferrodoxin_rbo.
[Graphical view]

KO

K05919.

Pfam

PF06397. Desulfoferrod_N. 1 hit.
PF01880. Desulfoferrodox. 1 hit.
[Graphical view]

SUPFAM

SSF49367. Desulfoferrodox. 1 hit.

TIGRFAMs

TIGR00319. Desulf_FeS4. 1 hit.
TIGR00320. Dfx_rbo. 1 hit.
TIGR00332. Neela_ferrous. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DFX_DESB2

Accession

Primary (citable) accession number: Q46495
Secondary accession number(s): E1QI98

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 87 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program