Superoxide dismutase

 

Copper-zinc superoxide dimutase (CuZnSOD) catalyses the disproportionation of superoxide into dioxygen and hydrogen peroxide.

In higher organisms, superoxide anions are produced as an occasional byproduct during the one-electron reduction of dioxygen in respiration and photosynthesis. Superoxides are also produced by macrophages as a part of the immune response. Excess amounts of superoxides can inactivate enzymes with iron-sulphur clusters and can lead to the formation of highly oxidising species that can damage cellular constituents. Therefore, organisms must have ways to regulate the concentration of superoxide concentrations. Many Gram-negative bacterial pathogens also possess CuZnSOD to counteract the phagocyte superoxide burst from their hosts.

 

Reference Protein and Structure

Sequence
P00445 UniProt (1.15.1.1) IPR001424 (Sequence Homologues) (PDB Homologues)
Biological species
Saccharomyces cerevisiae S288c (Baker's yeast) Uniprot
PDB
2jcw - REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE (1.7 Å) PDBe PDBsum 2jcw
Catalytic CATH Domains
2.60.40.200 CATHdb (see all for 2jcw)
Cofactors
Zinc(2+) (1), Copper(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.15.1.1)

superoxide
CHEBI:18421ChEBI
+
hydron
CHEBI:15378ChEBI
→
hydrogen peroxide
CHEBI:16240ChEBI
+
dioxygen
CHEBI:15379ChEBI
Alternative enzyme names: Cu,Zn-SOD, Cu-Zn superoxide dismutase, Fe-SOD, Mn-SOD, SOD, SOD-1, SOD-2, SOD-3, SOD-4, SODF, SODS, Copper-zinc superoxide dismutase, Cuprein, Cytocuprein, Erythrocuprein, Ferrisuperoxide dismutase, Hemocuprein, Hepatocuprein, Superoxidase dismutase, Superoxide dismutase I, Superoxide dismutase II,

Enzyme Mechanism

Introduction

Based on crystal structures, a mechanism is proposed. Guided by the electrostatic channel, superoxide enters the active site, displaces a water molecule, forms a hydrogen bond with Arg143 and binds to the copper(II) ion. Bound superoxide reduces Cu(II) to Cu(I) with simultaneous breaking of the bond between His63 and the Cu(I) ion. Dioxygen is released and His63 is protonated by the solvent. Another superoxide enters the active site. Electron is transferred from Cu(I) to the superoxide and at the same time, two protons are transferred to the superoxides from protonated His63 and a water molecule, forming hydrogen peroxide. Cu(II) then moves to reform the histidine bridge.

Zn(II) bound to His63 ND1 raises the pKa of NE2 to ~13, so that unliganded NE2 will always be protonated at physiological pH.

Catalytic Residues Roles

UniProt PDB* (2jcw)
His72, Asp84, His81 His71A, Asp83A, His80A Forms part of the zinc binding site. metal ligand
His64 His63A Acts as an acid to donate a proton to superoxide in the second part of the reaction cycle to form hydrogen peroxide. Acts as a bridging ligand between the structural zinc and catalytic copper ions. hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
Arg144 Arg143A Acts to stabilise the reactive intermediates. hydrogen bond donor, electrostatic stabiliser
His121, His47, His49 His120A, His46A, His48A Forms part of the copper binding site. metal ligand
*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

electron transfer, radical termination, proton transfer, cofactor used, coordination to a metal ion, native state of cofactor regenerated, native state of enzyme regenerated, proton relay

References

  1. Hart PJ et al. (1999), Biochemistry, 38, 2167-2178. A Structure-Based Mechanism for Copper−Zinc Superoxide Dismutase†,‡. DOI:10.1021/bi982284u. PMID:10026301.
  2. Maji RC et al. (2016), Dalton Trans, 45, 11898-11910. Electron transfer mechanism of catalytic superoxide dismutation via Cu(ii/i) complexes: evidence of cupric-superoxo/-hydroperoxo species. DOI:10.1039/c6dt02220k. PMID:27383660.
  3. Sea K et al. (2015), J Biol Chem, 290, 2405-2418. Insights into the Role of the Unusual Disulfide Bond in Copper-Zinc Superoxide Dismutase. DOI:10.1074/jbc.m114.588798. PMID:25433341.
  4. Szpryngiel S et al. (2015), FEBS Open Bio, 5, 56-63. Diffuse binding of Zn2+to the denatured ensemble of Cu/Zn superoxide dismutase 1. DOI:10.1016/j.fob.2014.12.003. PMID:25685664.
  5. Shin DS et al. (2009), J Mol Biol, 385, 1534-1555. Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis. DOI:10.1016/j.jmb.2008.11.031. PMID:19063897.
  6. Ferraroni M et al. (1999), J Mol Biol, 288, 413-426. The crystal structure of the monomeric human SOD mutant F50E/G51E/E133Q at atomic resolution. the enzyme mechanism revisited. DOI:10.1006/jmbi.1999.2681. PMID:10329151.
  7. Tainer JA et al. (1983), Nature, 306, 284-287. Structure and mechanism of copper, zinc superoxide dismutase. DOI:10.1038/306284a0. PMID:6316150.

Step 1. In the resting state of the enzyme, there is a water coordinated to the copper, analogous to the final state of this step, save that the histidine in the resting state is negatively charged and bound to the copper II ion. The superoxide gives up its electron to the Copper II ion. Dioxygen, no longer charged and electrostatically attracted to Arg143, diffuses out of the active site channel, and it is replaced by a water molecule, which starts of as a oxonium and concurrently gives up its proton to the His63, which breaks the histidine bridge [PMID:10026301

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His63A hydrogen bond acceptor
Arg143A electrostatic stabiliser
His63A metal ligand
Asp83A metal ligand
His71A metal ligand
His80A metal ligand
His48A metal ligand
His120A metal ligand
His46A metal ligand
His63A proton acceptor

Chemical Components

electron transfer, radical termination, proton transfer, cofactor used

Step 2. The second superoxide molecule enters the active site cavity, displaces a water molecule and hydrogen bonds with the protonated NE2 atom of His63 and a water molecule. A chain of water molecules can relay protons to the active site, replenishing those delivered to form peroxide. The neutral hydrogen peroxide is displaced from the active site by a water molecule to return the enzyme to its initial resting state

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His63A metal ligand
Asp83A metal ligand
His71A metal ligand
His80A metal ligand
His48A metal ligand
His120A metal ligand
His46A metal ligand
His63A hydrogen bond donor
Arg143A hydrogen bond donor, electrostatic stabiliser
His63A proton donor

Chemical Components

proton transfer, electron transfer, radical termination, coordination to a metal ion, native state of cofactor regenerated, native state of enzyme regenerated, proton relay
Download: Image, Marvin File

Step 1. In the resting state of the enzyme, there is a water coordinated to the copper, analogous to the final state of this step, save that the histidine in the resting state is negatively charged and bound to the copper II ion. The superoxide gives up its electron to the Copper II ion. Dioxygen, no longer charged and electrostatically attracted to Arg143, diffuses out of the active site channel, and it is replaced by a water molecule, which starts of as a oxonium and concurrently gives up its proton to the His63, which breaks the histidine bridge [PMID:10026301

Step 2. The second superoxide molecule enters the active site cavity, displaces a water molecule and hydrogen bonds with the protonated NE2 atom of His63 and a water molecule. A chain of water molecules can relay protons to the active site, replenishing those delivered to form peroxide. The neutral hydrogen peroxide is displaced from the active site by a water molecule to return the enzyme to its initial resting state

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Craig Porter, Mei Leung