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Literature summary for 1.15.1.2 extracted from

  • Pinto, A.; Rodrigues, J.; Teixeira, M.
    Reductive elimination of superoxide: Structure and mechanism of superoxide reductases (2010), Biochim. Biophys. Acta, 1804, 285-297.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
cloning of the desulfoferrodoxin, encoded adjacent to a gene encoding a type I rubredoxin forming a single transcriptional unit Desulfovibrio vulgaris
DNA and amino acid sequence analysis, phylogenetic tree Archaeoglobus fulgidus
DNA and amino acid sequence analysis, phylogenetic tree Treponema pallidum
DNA and amino acid sequence analysis, phylogenetic tree Desulfarculus baarsii
DNA and amino acid sequence analysis, phylogenetic tree Nanoarchaeum equitans
DNA and amino acid sequence analysis, phylogenetic tree Pyrococcus furiosus
DNA and amino acid sequence analysis, phylogenetic tree Desulfovibrio desulfuricans

Crystallization (Commentary)

Crystallization (Comment) Organism
crystal structure analysis of the native and ferricyanide bound wild-type enzyme, PDB ID 1DFX Desulfovibrio desulfuricans
crystal structure analysis of the native and Glu unbound wild-type enzyme, PDB ID 1Y07 Treponema pallidum
crystal structure analysis of the oxidized and Glu bound wild-type enzyme, PDB ID 2HVB Pyrococcus horikoshii
crystal structure analysis of the reduced or the oxidized and Glu bound wild-type enzyme, PDB IDs 1DQI, 1DO6, and 1DQK Pyrococcus furiosus
crystal structure analysis of the reduced wild-type enzyme, PDB ID 2AMU Thermotoga maritima
crystal structure analysis of the wild-type and E114A mutant enzymes in different oxidation states, PDB IDs 2JI3, 2JI2, 2JI1, and 1VZI Desulfarculus baarsii

Protein Variants

Protein Variants Comment Organism
E114A crystal structure Desulfarculus baarsii
E12V redox properties of the mutant compared to the wild-type enzyme Archaeoglobus fulgidus
E47A redox properties of the mutant compared to the wild-type enzyme Desulfovibrio vulgaris
E47A redox properties of the mutant compared to the wild-type enzyme Desulfarculus baarsii
K48A redox properties of the mutant compared to the wild-type enzyme Desulfovibrio vulgaris
K48A redox properties of the mutant compared to the wild-type enzyme Treponema pallidum
K48A redox properties of the mutant compared to the wild-type enzyme Desulfarculus baarsii

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information steady-state kinetics Megalodesulfovibrio gigas

Metals/Ions

Metals/Ions Comment Organism Structure
Iron 1Fe-SOR and 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 Archaeoglobus fulgidus
Iron 1Fe-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 Treponema pallidum
Iron 1Fe-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 Thermotoga maritima
Iron 1Fe-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 Pyrococcus horikoshii
Iron 1Fe-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. The electrostatic surface close to center II has a positive character, mainly due to the metal ion and to residue Lys 15 of 1Fe-SOR, metal site structure and mechanism, overview Pyrococcus furiosus
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 Desulfarculus baarsii
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 Desulfovibrio desulfuricans
Iron 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 Desulfovibrio vulgaris
Iron 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 Megalodesulfovibrio gigas
Iron 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 Nanoarchaeum equitans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
reduced rubredoxin + superoxide + 2 H+ Desulfovibrio vulgaris
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Archaeoglobus fulgidus
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Megalodesulfovibrio gigas
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Treponema pallidum
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Desulfarculus baarsii
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Nanoarchaeum equitans
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Pyrococcus furiosus
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Thermotoga maritima
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Pyrococcus horikoshii
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Desulfovibrio desulfuricans
-
rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+ Pyrococcus horikoshii OT-3
-
rubredoxin + H2O2
-
?

Organism

Organism UniProt Comment Textmining
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
-
-
-

Purification (Commentary)

Purification (Comment) Organism
isolation of center I and II Megalodesulfovibrio gigas

Reaction

Reaction Comment Organism Reaction ID
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, geometry of the catalytic center, oxidative cycle/reductive pathway, overview Pyrococcus furiosus
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, geometry of the catalytic center, oxidative cycle/reductive pathway, overview Desulfovibrio desulfuricans
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Desulfovibrio vulgaris
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Archaeoglobus fulgidus
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Megalodesulfovibrio gigas
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Treponema pallidum
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Desulfarculus baarsii
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Nanoarchaeum equitans
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Thermotoga maritima
superoxide + reduced rubredoxin + 2 H+ = H2O2 + oxidized rubredoxin reaction mechanism, oxidative cycle/reductive pathway, overview Pyrococcus horikoshii

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information redox properties of SOR's catalytic center, overview Archaeoglobus fulgidus ?
-
?
additional information redox properties of SOR's catalytic center, overview Megalodesulfovibrio gigas ?
-
?
additional information redox properties of SOR's catalytic center, overview Treponema pallidum ?
-
?
additional information redox properties of SOR's catalytic center, overview Desulfarculus baarsii ?
-
?
additional information redox properties of SOR's catalytic center, overview Nanoarchaeum equitans ?
-
?
additional information redox properties of SOR's catalytic center, overview Desulfovibrio desulfuricans ?
-
?
reduced rubredoxin + superoxide + 2 H+
-
Desulfovibrio vulgaris rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Archaeoglobus fulgidus rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Megalodesulfovibrio gigas rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Treponema pallidum rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Desulfarculus baarsii rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Nanoarchaeum equitans rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Pyrococcus furiosus rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Thermotoga maritima rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Pyrococcus horikoshii rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Desulfovibrio desulfuricans rubredoxin + H2O2
-
?
reduced rubredoxin + superoxide + 2 H+
-
Pyrococcus horikoshii OT-3 rubredoxin + H2O2
-
?

Subunits

Subunits Comment Organism
homodimer
-
Desulfarculus baarsii
homodimer the 1Fe-SOR from Treponema pallidum, which has an extra N-terminal domain reminiscent of those from 2Fe-SORs, is a homodimer Treponema pallidum
homodimer three-dimensional structure of SOR, overview Desulfovibrio desulfuricans
homotetramer
-
Archaeoglobus fulgidus
homotetramer
-
Nanoarchaeum equitans
homotetramer
-
Thermotoga maritima
homotetramer
-
Pyrococcus horikoshii
homotetramer 1Fe-SOR Pyrococcus furiosus
More three-dimensional structure of the neelaredoxin, overview Pyrococcus furiosus

Synonyms

Synonyms Comment Organism
1Fe-SOR
-
Archaeoglobus fulgidus
1Fe-SOR
-
Treponema pallidum
1Fe-SOR
-
Pyrococcus furiosus
1Fe-SOR
-
Thermotoga maritima
1Fe-SOR
-
Pyrococcus horikoshii
2Fe-SOR
-
Archaeoglobus fulgidus
2Fe-SOR
-
Desulfarculus baarsii
2Fe-SOR
-
Desulfovibrio desulfuricans
Dfx
-
Desulfovibrio desulfuricans
neelaredoxin
-
Pyrococcus furiosus
SOR
-
Desulfovibrio vulgaris
SOR
-
Archaeoglobus fulgidus
SOR
-
Megalodesulfovibrio gigas
SOR
-
Treponema pallidum
SOR
-
Desulfarculus baarsii
SOR
-
Nanoarchaeum equitans
SOR
-
Pyrococcus furiosus
SOR
-
Thermotoga maritima
SOR
-
Pyrococcus horikoshii
SOR
-
Desulfovibrio desulfuricans

Cofactor

Cofactor Comment Organism Structure
additional information structure of the neelaredoxin center, oxidized and reduced forms, overview Pyrococcus furiosus
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 Desulfovibrio vulgaris
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 Megalodesulfovibrio gigas
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 Desulfovibrio desulfuricans

General Information

General Information Comment Organism
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Desulfovibrio vulgaris
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Megalodesulfovibrio gigas
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Treponema pallidum
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Desulfarculus baarsii
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Nanoarchaeum equitans
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Pyrococcus furiosus
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Thermotoga maritima
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Pyrococcus horikoshii
physiological function SOR is responsible for reductive elimination of toxic superoxide as part of the detoxifying system Desulfovibrio desulfuricans
physiological function SOR is responsible for reductive eliminatioon of toxic superoxide as part of the detoxifying system Archaeoglobus fulgidus