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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1do6
Original Entry
Title:
Oxidoreductase
Compound:
Superoxide reductase
Mutant:
No
UniProt/Swiss-Prot:
P82385-SOR_PYRFU
EC Class:
1.15.1.2
Other CSA Entries:
Overview of all sites for 1do6
Homologues of 1do6
Entries for UniProt/Swiss-Prot: P82385
Entries for EC: 1.15.1.2
Other Databases:
PDB entry: 1do6
PDBsum entry: 1do6
UniProt/Swiss-Prot: P82385
IntEnz entry: 1.15.1.2
Literature Report:
Introduction:
Neelareductase, or superoxide reductase, from the thermophilic Archaea Pyrococcus furiosus, is able to catalyse the conversion of the superoxide radical O*- into the less toxic product hydrogen peroxide. It shares this ability with a number of homologous proteins from anaerobic bacteria and archaea where the removal of the superoxide radical, a product of anaerobic respiration in these organisms, is essential for their survival. It is part of a family of mononuclear non-haem iron containing proteins, which all have the iron coordinated with a pentacoordinate 4His Cys motif and a variable 6th ligand.
Mechanism:
The iron centre is able to reduce the superoxide radical to hydrogen peroxide, ultimately accepting electrons from a NADPH coupled oxidoreductase, thus transferring the electrons from NADPH to the superoxide radical. In doing so, the reduced iron centre Fe(II) gives an electron to the superoxide with concomitant protonation by Lys 15. This produces an intermediate Fe(III) hydroperoxide species which picks up another proton allowing hydrogen peroxide release, assisted by the binding of Glu 14 to the Fe (III) centre to replace the oxygen of the hydroperoxide as a ligand. Regeneration of the catalytic Fe (II) ion is then achieved by the donation of electrons from an NADPH oxidoreductase.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 14 14Sidechain
ElectrostaticTransition state
Acts as the 6th iron ligand when in the Fe (III) form, thus protecting this form from being reduced, and allowing hydrogen peroxide to leave the complex.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11489883 Related protein: O29903 Residue is positioned appropriately (ligand position known)
PubMed ID 11914081 Related protein: UniProt P20418 Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 15 15Sidechain
Acid/baseSubstrate
Protonates the superoxide radical to allow it to accept an electron from the iron centre, thus forming the hydroperoxide intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11914081 Related protein: UniProt P20418 Mutagenesis of residue
PubMed ID 11914081 Related protein: UniProt P20418 pH dependence of reaction
PubMed ID 10704199 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
FEA 200 0
Electron donor/acceptorSubstrate
Acts as an electron donor in the reaction, becoming oxidised from iron (II) to iron (III). This allows it to accept the hydroperoxide intermediate as a 6th ligand, thus stabilising it.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11489883 Related protein: O29903 Residue is covalently bound to intermediate, based on non-structural data
PubMed ID 10704199 Current protein Ligand is essential for catalysis
PubMed ID 10704199 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states.
A. P. Yeh and Y. Hu and F. E. Jenney and M. W. Adams and D. C. Rees
Biochemistry 39, (10) 2499-508, (2000).
10704199
2
Kinetics and mechanism of superoxide reduction by two-iron superoxide reductase from Desulfovibrio vulgaris.
J. P. Emerson and E. D. Coulter and D. E. Cabelli and R. S. Phillips and D. M. Kurtz
Biochemistry 41, (13) 4348-57, (2002).
11914081
3
The mechanism of superoxide scavenging by Archaeoglobus fulgidus neelaredoxin.
I. A. Abreu and L. M. Saraiva and C. M. Soares and M. Teixeira and D. E. Cabelli
J Biol Chem 276, (42) 38995-9001, (2001).
11489883
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