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Information on EC 1.15.1.2 - superoxide reductase and Organism(s) Desulfarculus baarsii and UniProt Accession Q46495

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IUBMB Comments
The enzyme contains non-heme iron.
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Desulfarculus baarsii
UNIPROT: Q46495
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Word Map
The taxonomic range for the selected organisms is: Desulfarculus baarsii
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
+
reduced rubredoxin
+
2
=
+
oxidized rubredoxin
Synonyms
superoxide reductase, neelaredoxin, desulfoferrodoxin, desulforedoxin, rubredoxin oxidoreductase, 2fe-sor, pfsor, 1fe-sor, two-iron superoxide reductase, gisor, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
desulfoferrodoxin
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rubredoxin oxidoreductase
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desulfoferrodoxin
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desulforedoxin
-
-
-
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superoxide reductase
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two-iron superoxide reductase
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-
additional information
the enzyme belongs to the class I of superoxide reductases
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin
show the reaction diagram
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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-
-
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oxidation
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-
-
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reduction
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-
-
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PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
rubredoxin:superoxide oxidoreductase
The enzyme contains non-heme iron.
CAS REGISTRY NUMBER
COMMENTARY hide
250679-67-5
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
reduced rubredoxin + superoxide + 2 H+
rubredoxin + H2O2
show the reaction diagram
the active site consists of an unusual non-heme Fe2+ center in a [His4 Cys1] square pyramidal pentacoordination, the reaction procedes via a Fe3+-peroxo intermediate
-
-
?
reduced rubredoxin + superoxide + H+
rubredoxin + H2O2
show the reaction diagram
superoxide + reduced acceptor + 2 H+
H2O2 + oxidized acceptor
show the reaction diagram
-
-
-
?
reduced cytochrome c + superoxide + H+
cytochrome c + H2O2
show the reaction diagram
-
enzyme shows only very weak superoxide dismutase activity
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-
?
reduced rubredoxin + superoxide + 2 H+
rubredoxin + H2O2
show the reaction diagram
superoxide + reduced rubredoxin + 2 H+
H2O2 + oxidized rubredoxin
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
reduced rubredoxin + superoxide + H+
rubredoxin + H2O2
show the reaction diagram
superoxide + reduced acceptor + 2 H+
H2O2 + oxidized acceptor
show the reaction diagram
-
-
-
?
reduced rubredoxin + superoxide + 2 H+
rubredoxin + H2O2
show the reaction diagram
-
-
-
-
?
superoxide + reduced rubredoxin + 2 H+
H2O2 + oxidized rubredoxin
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
in contrast to superoxide dismutases, EC 1.15.1.1, SORs do not catalyze the dismutation reaction of superoxide, but catalyze a one-electron reduction of superoxide to produce H2O2, without formation of O2, electron transfer mechanisms, detailed overview
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
reduced rubredoxin
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rubredoxin
-
-
-
additional information
-
the active site consists of an unusual mononuclear iron center with an FeN4S1 coordination which catalyzes the one electron reduction of superoxide to form hydrogen peroxide. Presence of an additional rubredoxin-like desulforedoxin iron center, that functions as an electronic relay between cellular reductases and the iron active site for superoxide reduction
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe
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2Fe-SOR contains iron center I and iron center II, function of iron center I as an electronic relay between a reductase enzyme and iron center II, overview. The active site consists of an unusual mononuclear iron center with an FeN4S1 coordination which catalyzes the one electron reduction of superoxide to form hydrogen peroxide. Presence of an additional rubredoxin-like desulforedoxin iron center, which functions as an electronic relay between cellular reductases and the iron active site for superoxide reduction
Fe2+
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SOR is a small non-heme mononuclear iron protein, formation of high-valent iron-oxo species in superoxide reductase, analysis by resonance Raman spectroscopy, overview
Fe2+/Fe3+
additional information
binding of synthetic iron ligand complexes, overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.6
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
Fe-SOR classification, detailed overview. One classification takes into consideration the primary and tertiary structures of SORs some enzymes contain only one Fe ion, but have a longer N-terminus with amino acid sequence and structural similarities with those of the respective domain of desulfoferrodoxins, but lacking the cysteine ligands to the desulforedoxin (Dfxs)-like center. According to the authors, SORs fall into three classes: classes I (Dfxs), II (neelaredoxins), and III (neelaredoxins structurally homologous to desulfoferrodoxins, with only one Fe center). In dendograms constructed from available amino acid sequences, class III enzymes cluster within the class I enzymes, it is plausible that class III SORs evolved from class I proteins by loss of the cysteine residues binding the desulforedoxin-like center, an event that may have occurred more than once because the Dfxs are not monophyletic. This classification misses the family of methanoferrodoxins. Another classification is based on the variability of N-terminal domains classifying SORs into seven classes. Class I or Dx-SOR includes the 2Fe-SORs, where the N-terminal is a desulforedoxin-like (Dx) domain. Class II includes the 1Fe-SORs that have no extra N-terminal domain. Class III SORs are analogous to Dx-SORs but lacking some or all of the Fe cysteine ligands (FeCys4) for the desulforedoxin-like Fe center and therefore lacking the FeCy4 site. Class IV includes SORs with an extra C-terminal domain containing an iron-sulfur center. The fifth class, termed HTH-Dx-SOR, includes Dx-SORs (2Fe-SOR) with an extended N-terminal helix-turn-helix domain present in transcription regulators. The sixth class, termed TAT-SOR, includes SORs from only a few organisms and the sequences are preceded by a putative twin-arginine signal peptide that suggests their periplasmic localization
malfunction
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mutation of two residues in the second coordination sphere of the SOR iron active site, K48 and I118, leads to the formation of a high-valent iron-oxo species when the mutant proteins are reacted with H2O2
physiological function
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14028
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2 * 14028, ES-MS
27000
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gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
homodimer
additional information
structure-function relationship, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structures determination of wild/tzp and mutant enzymes at 1.15-1.95 A resolution, PDB IDs 1VZI, 1VZG, 1VZH, 2JI1, 2JI2, and 2JI3
crystallization of the recombinant enzyme
mutant E47A, alone and in complex with ferrocyanide, the iron in the actice site is coordinated through a bent cyano bridge
crystal structure analysis of the wild-type and E114A mutant enzymes in different oxidation states, PDB IDs 2JI3, 2JI2, 2JI1, and 1VZI
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E114A
E46A
site-directed mutagenesis, crystal structure determination
K48I
site-directed mutagenesis
C13S
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site-directed mutagenesis, the lack of iron center I in the C13S SOR mutant does not significantly affect the folding of iron center II and its reactivity with superoxide
E114A
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crystal structure
I118S
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site-directed mutagenesis, the mutat shows an altered active site compared to the wild-type and formation of a high-valent iron-oxo species when the mutant protein is reacted with H2O2.. For I118S, formation of the iron-oxo species can also result from the cleavage of the O-O bond of an FeIII-OOH intermediate
K48A
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redox properties of the mutant compared to the wild-type enzyme
Y115A
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site-directed mutagenesis, the Y115A SOR mutant folds properly, this mutation does not affect the general properties of the two iron sites of SOR
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme with a fully oxidized metal center I
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recombinant enzyme, gel filtration, anion exchange
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recombinant wild-type and mutant SORs, and rubredoxin from Escherichia coli strain BL21(DE3) to homogeneity by anion exchange chromatography and gel filtration
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so far there is no suitable enzymatic assay for monitoring the purification from cell extracts
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wild-type and E47A and K48I mutant enzyme
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of class I Dfx, phylogenetic analysis
gene sor, complementation of the Escherichia coli QC2375 mutant strain
DNA and amino acid sequence analysis, phylogenetic tree
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expression in Escherichia coli
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expression of wild-type and mutant SORs, and of rubredoxin in Escherichia coli strain BL21(DE3)
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recombinant expression
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lombard, M.; Fontecave, M.; Touati, D.; Niviere, V.
Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with superoxide anion. Evidence for a superoxide reductase activity
J. Biol. Chem.
275
115-121
2000
Desulfarculus baarsii
Manually annotated by BRENDA team
Lombard, M.; Houee-Levin, C.; Touati, D.; Fontecave, M.; Niviere, V.
Superoxide reductase from Desulfoarculus baarsii: reaction mechanism and role of glutamate 47 and lysine 48 in catalysis
Biochemistry
40
5032-5040
2001
Desulfarculus baarsii
Manually annotated by BRENDA team
Mathe, C.; Mattioli, T.A.; Horner, O.; Lombard, M.; Latour, J.M.; Fontecave, M.; Niviere, V.
Identification of iron(III) peroxo species in the active site of the superoxide reductase SOR from Desulfoarculus baarsii
J. Am. Chem. Soc.
124
4966-4967
2002
Desulfarculus baarsii
Manually annotated by BRENDA team
Rusnak, F.; Ascenso, C.; Moura, I.; Moura, J.J.G.
Superoxide reductase activities of neelaredoxin and desulfoferrodoxin metalloproteins
Methods Enzymol.
349
243-258
2002
Archaeoglobus fulgidus, Desulfarculus baarsii, Desulfovibrio vulgaris, Pyrococcus furiosus, Treponema pallidum
Manually annotated by BRENDA team
Niviere, V.; Lombard, M.
Superoxide reductase from Desulfoarculus baarsii
Methods Enzymol.
349
123-129
2002
Desulfarculus baarsii, Treponema pallidum
Manually annotated by BRENDA team
Berthomieu, C.; Dupeyrat, F.; Fontecave, M.; Vermeglio, A.; Niviere, V.
Redox-dependent structural changes in the superoxide reductase from Desulfoarculus baarsii and Treponema pallidum: a FTIR study
Biochemistry
41
10360-10368
2002
Desulfarculus baarsii
Manually annotated by BRENDA team
Niviere, V.; Asso, M.; Weill, C.O.; Lombard, M.; Guigliarelli, B.; Favaudon, V.; Houee-Levin, C.
Superoxide reductase from Desulfoarculus baarsii: identification of protonation steps in the enzymatic mechanism
Biochemistry
43
808-818
2004
Desulfarculus baarsii
Manually annotated by BRENDA team
Adam, V.; Royant, A.; Niviere, V.; Molina-Heredia, F.P.; Bourgeois, D.
Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction
Structure
12
1729-1740
2004
Desulfarculus baarsii (Q46495), Desulfarculus baarsii
Manually annotated by BRENDA team
Mathe, C.; Niviere, V.; Houee-Levin, C.; Mattioli, T.A.
Fe(3+)-eta(2)-peroxo species in superoxide reductase from Treponema pallidum. Comparison with Desulfoarculus baarsii
Biophys. Chem.
119
38-48
2006
Desulfarculus baarsii, Treponema pallidum
Manually annotated by BRENDA team
Mathe, C.; Niviere, V.; Mattioli, T.A.
Fe3+-hydroxide ligation in the superoxide reductase from Desulfoarculus baarsii is associated with pH dependent spectral changes
J. Am. Chem. Soc.
127
16436-16441
2005
Desulfarculus baarsii
Manually annotated by BRENDA team
Molina-Heredia, F.P.; Houee-Levin, C.; Berthomieu, C.; Touati, D.; Tremey, E.; Favaudon, V.; Adam, V.; Niviere, V.
Detoxification of superoxide without production of H2O2: antioxidant activity of superoxide reductase complexed with ferrocyanide
Proc. Natl. Acad. Sci. USA
103
14750-14755
2006
Desulfarculus baarsii
Manually annotated by BRENDA team
Kovacs, J.A.; Brines, L.M.
Understanding how the thiolate sulfur contributes to the function of the non-heme iron enzyme superoxide reductase
Acc. Chem. Res.
40
501-509
2007
Desulfarculus baarsii (Q46495)
Manually annotated by BRENDA team
Pereira, A.S.; Tavares, P.; Folgosa, F.; Almeida, R.M.; Moura, I.; Moura, J.J.
Superoxide reductases
Eur. J. Inorg. Chem.
2007
2569-2581
2007
Archaeoglobus fulgidus (O29903), Desulfarculus baarsii (Q46495), Desulfovibrio desulfuricans, Desulfovibrio vulgaris (P20418), Megalodesulfovibrio gigas, Methanothermobacter thermautotrophicus, Pyrococcus furiosus (P82385), Thermotoga maritima (Q9WZC6), Treponema pallidum
-
Manually annotated by BRENDA team
Brines, L.M.; Kovacs, J.A.
Understanding the mechanism of superoxide reductase promoted reduction of superoxide
Eur. J. Inorg. Chem.
2007
29-38
2007
Desulfovibrio desulfuricans, Treponema palladium, Pyrococcus furiosus (P82385), Desulfarculus baarsii (Q46495)
-
Manually annotated by BRENDA team
Mathe, C.; Weill, C.O.; Mattioli, T.A.; Berthomieu, C.; Houee-Levin, C.; Tremey, E.; Niviere, V.
Assessing the role of the active-site cysteine ligand in the superoxide reductase from Desulfoarculus baarsii
J. Biol. Chem.
282
22207-22216
2007
Desulfarculus baarsii (Q46495), Desulfarculus baarsii
Manually annotated by BRENDA team
Pinto, A.; Rodrigues, J.; Teixeira, M.
Reductive elimination of superoxide: Structure and mechanism of superoxide reductases
Biochim. Biophys. Acta
1804
285-297
2010
Archaeoglobus fulgidus, Desulfarculus baarsii, Desulfovibrio desulfuricans (P22076), Desulfovibrio vulgaris, Megalodesulfovibrio gigas, Nanoarchaeum equitans, Pyrococcus furiosus (P82385), Pyrococcus horikoshii (O58810), Pyrococcus horikoshii OT-3 (O58810), Thermotoga maritima (Q9WZC6), Treponema pallidum
Manually annotated by BRENDA team
Bonnot, F.; Houee-Levin, C.; Favaudon, V.; Niviere, V.
Photochemical processes observed during the reaction of superoxide reductase from Desulfoarculus baarsii with superoxide. Re-evaluation of the reaction mechanism
Biochim. Biophys. Acta
1804
762-767
2010
Desulfarculus baarsii
Manually annotated by BRENDA team
Bonnot, F.; Duval, S.; Lombard, M.; Valton, J.; Houee-Levin, C.; Niviere, V.
Intermolecular electron transfer in two-iron superoxide reductase: a putative role for the desulforedoxin center as an electron donor to the iron active site
J. Biol. Inorg. Chem.
16
889-898
2011
Desulfarculus baarsii
Manually annotated by BRENDA team
Bonnot, F.; Tremey, E.; von Stetten, D.; Rat, S.; Duval, S.; Carpentier, P.; Clemancey, M.; Desbois, A.; Niviere, V.
Formation of high-valent iron-oxo species in superoxide reductase characterization by resonance Raman spectroscopy
Angew. Chem. Int. Ed. Engl.
53
5926-5930
2014
Desulfarculus baarsii, Desulfarculus baarsii ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14
Manually annotated by BRENDA team
Sheng, Y.; Abreu, I.; Cabelli, D.; Maroney, M.; Miller, A.; Teixeira, M.; Valentine, J.
Superoxide dismutases and superoxide reductases
Chem. Rev.
114
3854-3918
2014
Archaeoglobus fulgidus, Archaeoglobus fulgidus (O29903), Archaeoglobus fulgidus ATCC 49558 (O29903), Desulfarculus baarsii (Q46495), Desulfarculus baarsii ATCC 33931 (Q46495), Desulfovibrio desulfuricans, Desulfovibrio vulgaris, Dosidicus gigas, Ignicoccus hospitalis (A8AC72), Ignicoccus hospitalis KIN4/I / DSM 18386 / JCM 14125 (A8AC72), Nanoarchaeum equitans (Q74MF3), Pyrococcus furiosus (P82385), Pyrococcus furiosus ATCC 43587 (P82385), Pyrococcus horikoshii (O58810), Thermotoga maritima (Q9WZC6), Thermotoga maritima ATCC 43589 (Q9WZC6), Treponema pallidum (O82795), Treponema pallidum Nichols (O82795)
Manually annotated by BRENDA team