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Information on EC 1.15.1.2 - superoxide reductase and Organism(s) Desulfovibrio desulfuricans and UniProt Accession P22076

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IUBMB Comments
The enzyme contains non-heme iron.
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Desulfovibrio desulfuricans
UNIPROT: P22076
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The taxonomic range for the selected organisms is: Desulfovibrio desulfuricans
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide
superoxide
+
reduced rubredoxin
+
2
H+
=
H2O2
+
oxidized rubredoxin
+
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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desulforedoxin
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-
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rubredoxin oxidoreductase
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-
additional information
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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
reaction mechanism, geometry of the catalytic center, oxidative cycle/reductive pathway, overview
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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oxidation
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reduction
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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
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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
-
-
-
?
reduced rubredoxin + superoxide + H+
rubredoxin + H2O2
show the reaction diagram
superoxide + reduced acceptor + 2 H+
H2O2 + oxidized acceptor
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 + 2 H+
rubredoxin + H2O2
show the reaction diagram
-
-
-
?
reduced rubredoxin + superoxide + H+
rubredoxin + H2O2
show the reaction diagram
-
-
-
-
?
superoxide + reduced acceptor + 2 H+
H2O2 + oxidized acceptor
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
reduced rubredoxin
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additional information
the enzyme contains two iron sites: center I, similar to that of desulforedoxin, a small iron protein having a rubredoxin-like FeCys4 center, and center II, another type of iron site, which is named desulfoferrodoxin, Dfx, or rubredoxin. Structure of the FeCys4 center I, oxidized and reduced forms. overview
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
2Fe-SOR, an iron ion is bound at the catalytic site to four histidines and a cysteine that, in its reduced form, reacts with superoxide anion with a diffusion-limited second order rate constant, metal site structure and mechanism, overview
Ca2+
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at the dimer interface coordinated by eight oxygen atoms, Ser87, Thr89 from both monomers, and two water molecules
additional information
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binding of synthetic iron ligand complexes, overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system
evolution
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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
additional information
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key catalytic residues are E47 and K48, catalytic Fe2+ binding residues are H49, H69, H74, C115, and H118
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
three-dimensional structure of SOR, overview
dimer
additional information
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structure-function relationship, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis of the native and ferricyanide bound wild-type enzyme, PDB ID 1DFX
crystal structure determination at 1.9 A resolution, PDB ID 1DFX
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crystallization of the native enzyme, X-ray diffraction structure determination and analysis at 1.9 A resolution, modelling
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E47A
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site-directed mutagenesis
E48A
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site-directed mutagenesis
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence analysis, phylogenetic tree
phylogenetic analysis
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
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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)
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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
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