Superoxide reductase

 

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 4 His Cys motif and a variable 6th ligand.

 

Reference Protein and Structure

Sequence
P82385 UniProt (1.15.1.2) IPR002742 (Sequence Homologues) (PDB Homologues)
Biological species
Pyrococcus furiosus DSM 3638 (Archaea) Uniprot
PDB
1do6 - CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE AT 2.0 ANGSTROM RESOLUTION (2.0 Å) PDBe PDBsum 1do6
Catalytic CATH Domains
2.60.40.730 CATHdb (see all for 1do6)
Cofactors
Iron(2+) (1), Iron(3+) (1)
Click To Show Structure

Enzyme Reaction (EC:1.15.1.2)

iron(2+)
CHEBI:29033ChEBI
+
hydron
CHEBI:15378ChEBI
+
superoxide
CHEBI:18421ChEBI
→
hydrogen peroxide
CHEBI:16240ChEBI
+
iron(3+)
CHEBI:29034ChEBI
Alternative enzyme names: Desulfoferrodoxin, Neelaredoxin,

Enzyme Mechanism

Introduction

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.

Catalytic Residues Roles

UniProt PDB* (1do6)
Glu14 Glu14A 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. nucleophile, metal ligand, electrostatic stabiliser
Lys15 Lys15A Protonates the superoxide radical to allow it to accept an electron from the iron centre, thus forming the hydroperoxide intermediate. proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

coordination to a metal ion, electron transfer, redox reaction, proton transfer, intermediate formation, overall product formed, native state of enzyme regenerated, intermediate terminated

References

  1. Abreu IA et al. (2001), J Biol Chem, 276, 38995-39001. The Mechanism of Superoxide Scavenging byArchaeoglobus fulgidus Neelaredoxin. DOI:10.1074/jbc.m103232200. PMID:11489883.
  2. Silaghi-Dumitrescu R et al. (2003), Inorg Chem, 42, 446-456. Computational Study of the Non-Heme Iron Active Site in Superoxide Reductase and Its Reaction with Superoxide. DOI:10.1021/ic025684l.
  3. Emerson JP et al. (2002), Biochemistry, 41, 4348-4357. Kinetics and Mechanism of Superoxide Reduction by Two-Iron Superoxide Reductase fromDesulfovibriovulgaris†. DOI:10.1021/bi0119159. PMID:11914081.
  4. Yeh AP et al. (2000), Biochemistry, 39, 2499-2508. Structures of the Superoxide Reductase fromPyrococcus furiosusin the Oxidized and Reduced States†,‡. DOI:10.1021/bi992428k. PMID:10704199.

Step 1. The superoxide radical binds to the iron centre, oxidising Fe(II) to Fe(III).

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His16A metal ligand
His41A metal ligand
His47A metal ligand
Cys111A metal ligand
His114A metal ligand

Chemical Components

coordination to a metal ion, electron transfer, redox reaction

Step 2. The superoxide is protonated by Lys15.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His41A metal ligand
His47A metal ligand
Cys111A metal ligand
His114A metal ligand
Glu14A electrostatic stabiliser
Lys15A proton donor

Chemical Components

proton transfer, intermediate formation

Step 3. The hydroperoxy intermediate is protonated again and released from the iron centre by Glu14. The Fe(II) centre is subsequently regenerated by the donation of electrons from an NADPH oxidoreductase.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu14A metal ligand
His16A metal ligand
His41A metal ligand
His47A metal ligand
Cys111A metal ligand
His114A metal ligand
Glu14A nucleophile

Chemical Components

overall product formed, coordination to a metal ion, native state of enzyme regenerated, intermediate terminated
Download: Image, Marvin File

Step 1. The superoxide radical binds to the iron centre, oxidising Fe(II) to Fe(III).

Step 2. The superoxide is protonated by Lys15.

Step 3. The hydroperoxy intermediate is protonated again and released from the iron centre by Glu14. The Fe(II) centre is subsequently regenerated by the donation of electrons from an NADPH oxidoreductase.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, Amelia Brasnett