Information on EC 1.15.1.2 - superoxide reductase

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The expected taxonomic range for this enzyme is: Archaea, Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.15.1.2
-
RECOMMENDED NAME
GeneOntology No.
superoxide reductase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
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reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
non-pathway related
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-
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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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
ATCC824, gene cac2450
UniProt
Manually annotated by BRENDA team
Desulfarculus baarsii ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14
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-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Ignicoccus hospitalis KIN4/I / DSM 18386 / JCM 14125
-
UniProt
Manually annotated by BRENDA team
Treponema palladium
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
reduced acceptor + superoxide
acceptor + H2O2 + O2
show the reaction diagram
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enzyme is able to both reduce and dismutate superoxide
-
?
reduced acceptor + superoxide + H+
acceptor + H2O2
show the reaction diagram
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enzyme can be fully reduced upon addition of NADH or NADPH under anaerobic conditions
-
?
reduced cytochrome c + superoxide + 2 H+
oxidized cytochrome c + H2O2
show the reaction diagram
reduced cytochrome c + superoxide + H+
cytochrome c + H2O2
show the reaction diagram
reduced desulforedoxin + superoxide + 2 H+
desulforedoxin + H2O2
show the reaction diagram
reduced rubredoxin + superoxide + 2 H+
oxidized rubredoxin + H2O2
show the reaction diagram
reduced rubredoxin + superoxide + 2 H+
rubredoxin + H2O2
show the reaction diagram
reduced rubredoxin + superoxide + H+
oxidized 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
superoxide + reduced rubredoxin + 2 H+
H2O2 + oxidized rubredoxin
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
reduced desulforedoxin + superoxide + 2 H+
desulforedoxin + H2O2
show the reaction diagram
reduced rubredoxin + superoxide + 2 H+
rubredoxin + H2O2
show the reaction diagram
reduced rubredoxin + superoxide + H+
oxidized 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
superoxide + reduced rubredoxin + 2 H+
H2O2 + oxidized rubredoxin
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cytochrome c
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artificial electron carrier
desulforedoxin
reduced rubredoxin
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rubredoxin
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additional information
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
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at the dimer interface coordinated by eight oxygen atoms, Ser87, Thr89 from both monomers, and two water molecules
Fe2+/Fe3+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetate
azide
cyanide
Zn-substituted rubredoxin
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generation of Zn-substituted rubredoxin, which is diamagnetic and redox inactive, titration of Zn-rubredoxin with superoxide reductase, overview
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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analysis of reaction mechanism using synthetic construct [Fe(II)(SMe2N4(tren))]+ and a single peroxide intermediate, [Fe(III)(SMe2N4(tren))(OOH)]+
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0004
Zn-substituted rubredoxin
Desulfovibrio gigas;
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pH 7.6, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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60.0 U/mg, 1 U is the amount of enzyme necessary to inhibit 50% of the reduction of cytochrome c by the xanthine/xanthine oxidase system, superoxid dismutase activity of native enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8
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assay at
7.3
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assay at
additional information
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ionic strength dependence of superoxide-mediated rubredoxin oxidation
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 37
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assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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enzyme functions efficiently in vitro at 25°C, which is 75°C below the organism's optimal growth temperature
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
recombinant enzyme within midgut proteins extracted from transgenic Bombyx mori strain A4SOR and nontransgenic strain Dazao larvae on day 3 of the fifth instar
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126);
Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14);
V6TJK7
Giardia intestinalis;
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1);
O58810
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3);
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099);
O83795
Treponema pallidum (strain Nichols);
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
13670
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1 * 13800 + 1 * 13670, ESI-MS
13700
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x * 13700, recombinant enzyme
13800
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1 * 13800 + 1 * 13670, ESI-MS
14028
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2 * 14028, ES-MS
14300
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4 * 14300
14323
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x * 14323, deduced from nucleotide sequence
15000
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2 * 15000, SDS-PAGE
19000
gel filtration
20000
x * 20000, SDS-PAGE
26000
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gel filtration
27000
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gel filtration
30000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
homotetramer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, mixing of 0.0001 ml of 15 mg/ml protein in 20 mM phosphate buffer, pH 7.5, and 150 mM NaCl, with 0.0001 ml of reservoir solution, equilibration against 0.1 ml reservoir solution, vapour diffusion method, 2-3 days, method variantions, overview. X-ray diffraction structure determination and analysis at 1.9-2.4 A resolution, MAD method
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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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crystal structures determination of wild/tzp and mutant enyzmes at 1.15-1.95 A resolution, PDB IDs 1VZI, 1VZG, 1VZH, 2JI1, 2JI2, and 2JI3
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crystallization of the recombinant enzyme
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mutant E47A, alone and in complex with ferrocyanide, the iron in the actice site is coordinated through a bent cyano bridge
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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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purified enzyme, hanging drop vapour diffusion technique, mixing of 0.001 ml of 12 mg/ml protein solution in a 1:1 ratio with reservoir solution, and equilibration against 0.1 ml reservoir solution, method optimization, best crystals are obtained after 1 d in 24% v/v dioxane at protein:precipitant ratios of 0.002:0.0001, 0.0025:0.0001 and 0.003:0.0001 ml, 35% w/v glycerol is added to the cover slip to avoid dioxane evaporation, to a final volume of 0.006-0.010 ml, X-ray diffraction structure determination and analysis at 1.9-2.65 A resolution, modeling
crystal structure analysis, PDB ID 4BK8, modeling
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crystallization of purified recombinant oxidized 1Fe-SOR at room temperature, by sitting-drop vapour-diffusion method, mixing of 15 mg/ml protein in 20 mM Tris-HCl pH 7.2, 150 mM NaCl, with different drop mixing ratios of protein and reservoir solutions, method optimization to hanging drop vapour diffusion method, mixing of 0.002 ml of protein solution with 0.0005 ml of reservoir solution containing 85 mM Tris, pH 8.5, 8.5 mM NiCl2, 15% v/v PEG 2000 MME, and 15% v/v glycerol, X-ray diffraction structure determination and analysis of the blue crystals at 2.4 A resolution
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crystal structure analysis of the reduced or the oxidized and Glu bound wild-type enzyme, PDB IDs 1DQI, 1DO6, and 1DQK
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crystal structure determination at 2.0 A and 1.7 A resolution, respectively, PDB IDs 1DO6 and 1DQI
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crystallization of the recombinant and the native enzyme
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sitting drop vapor diffusion method
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crystal structure analysis of the oxidized and Glu bound wild-type enzyme, PDB ID 2HVB
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crystal structure determination at 2.5 A resolution, PDB ID 2HVB
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crystal structure analysis of the reduced wild-type enzyme, PDB ID 2AMU
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crystal structure determination at 2.0 A and 1.1 A resolution, respectively, PDB IDs 2AMU and 3QZB
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crystallization of the recombinant enzyme
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crystal structure analysis of the native and Glu unbound wild-type enzyme, PDB ID 1Y07
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crystal structure determination at 1.55 A resolution, PDB ID 1Y07
crystallization of the recombinant enzyme
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in presence of polyethylene glycol and magnesium chloride. Crystals grown in presence of K3Fe(CN)6 belong to space group P21 and diffract belong 1.6 A resolution, crystals grown in presence of Na2IrCl6 belong to space group C2 and diffract beyond 1.55 A
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protein lacks the N-terminal domain with the desulforedoxin-type iron centre known from other soperoxide reductases. Lack of the iron centre causes a decrease in the cohersion of the domain and some disorder. The C-terminal domain shows the characteristic immunoglobulin-like fold and harbours the Fe(His)4(cys) active centre
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
the thermal stability of the protein is significantly higher in 100 mM 3-(N-morpholino)-propanesulfonic acid (MOPS), pH 7.0, compared to 50 mM Tris-HCl, pH 7.5
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
isolation of center I and II
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native and recombinant enzyme
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recombinant Dfx from Escherichia coli strain BL21 by anion exchange chromatography, ultrafiltration, and gel filtration; recombinant enzyme
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recombinant enzyme
recombinant enzyme from Escherichia coli by anion exchange chromatography, ultrafiltration, and gel filtration
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recombinant enzyme from Escherichia coli strain BL21(DE3) by ultracentrifugation, anion exchange chromatography, and gel filtration
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recombinant enzyme with a fully oxidized metal center I
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recombinant enzyme, gel filtration, anion exchange
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by anion exchange and metal-chelate affinity chromatography
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recombinant His-tagged enzyme to homogeneity from Escherichia coli strain BL21-Gold (DE3) by nickel affinity chromatography, gel filtration and cleavage of the His-tag, followed by a second time nickel affinity chromatography and gel filtration
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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 K48A mutant
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wild-type and E47A and K48I mutant enzyme
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning of the desulfoferrodoxin, encoded adjacent to a gene encoding a type I rubredoxin forming a single transcriptional unit
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DNA and amino acid sequence analysis, phylogenetic tree
expressed as recombinant protein in Escherichia coli
expression in Escherichia coli
expression in Escherichia coli strain BL21(DE3)
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expression in Escherichia coli strain BL21-Gold (DE3)
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expression of class I Dfx, phylogenetic analysis
expression of class II Nlr and of class I Dfx, phylogenetic analysis
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expression of class II Nlr, phylogenetic analysis
expression of class III enzyme in Escherichia coli, phylogenetic analysis
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expression of Dfx in Escherichia coli strain BL21
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expression of wild-type and mutant enzymes in Escherichia coli strain XL2Blue
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expression of wild-type and mutant SORs, and of rubredoxin in Escherichia coli strain BL21(DE3)
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gene dsr, expression of class II Nlr in Escherichia coli, phylogenetic analysis
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gene nlr, DNA and amino acid sequence determination and analysis, subcloning in Escherichia coli strain XL-2 Blue, expression in Escherichia coli strain BL21(DE3)
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gene rbo, expression of class I Dfx, phylogenetic analysis
gene sor, complementation of the Escherichia coli QC2375 mutant strain
overexpression in Escherichia coli strain BL21(DE3)-Gold
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overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
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PfSOR, synthesis of an artificial DNA sequence (referred to as SOR-as) based on the PfSOR gene sequence No AE010234 and on codon bias of Bombyx mori and expression as FLAG-tagged enzyme in transgenic Bombyx mori strain A4SOR and in Bombyx mori BmE cells, the A4SOR insertion occurs on chromosome 10 in an intergenic region separated from the nearest genes to the left and right by 22 and 47 kb, respectively, Non-diapausing DZ embryos are microinjected with pb-A4SOR. Construction of vector 1180-hr3-A4P-Flag-SOR-His-SV4 and functionalrecombinant overexpression of C-terminally His-tagged enzyme, RT-PCR enzyme expression analysis and patterns in recombinant cells and transgenic in 8-day-old eggs, hatched silkworms, first instar molts, second instar larvae, second instar molts, third instar larvae, third instar molts, fourth instar larvae, fourth instar molts, fifth instar larvae, wandering silkworm, and pupae, overview
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phylogenetic analysis
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recombinant expression
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the enzyme can be produced as a functional enzyme in planta and that plants producing SOR have enhanced tolerance to heat, light, and chemically induced reactive oxygen species
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the enzyme is heterologously overexpressed in Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
activity remains essentially unchanged with change in the growth condition (maltose + peptides, maltose, maltose + peptides + sulfur S(0), maltose + sulfur S(0), peptides + sulfur S(0))
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
E46A
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site-directed mutagenesis, crystal structure determination
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
E114A
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site-directed mutagenesis, crystal structure determination
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E46A
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site-directed mutagenesis, crystal structure determination
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E47A
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site-directed mutagenesis, crystal structure determination
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K48I
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site-directed mutagenesis
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I118S
Desulfarculus baarsii ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14
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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
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K48I
Desulfarculus baarsii ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14
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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 the K48I mutant, the Fe=O species is formed from the FeIII-OOH species
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E47A
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site-directed mutagenesis
E48A
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site-directed mutagenesis
E47A
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site-directed mutagenesis
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E48A
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site-directed mutagenesis
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E48A
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site-directed mutagenesis
E23A
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site-directed mutagenesis
T24K
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site-directed mutagenesis
E23A
Ignicoccus hospitalis KIN4/I / DSM 18386 / JCM 14125
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site-directed mutagenesis
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T24K
Ignicoccus hospitalis KIN4/I / DSM 18386 / JCM 14125
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site-directed mutagenesis
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P8E
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site-directed mutagenesis, pH-induced transition of the mutant is similar to the wild-type enzyme, the reactivity of the N. equitans P8E Nlr mutant towards superoxide measured at different pHs is identical to that of the wild-type protein
E48A
site-directed mutagenesis
K48A
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redox properties of the mutant compared to the wild-type enzyme
E48A
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site-directed mutagenesis
-
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
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expression in Nicotiana tabacum as fusion protein with green fluorescent protein. Enzyme construct localizes to cytosol and nucleus. Enzyme retains its function and heat stability. Plant cells expressing the enzyme show enhanced survival at high temperatures
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