Superoxide dismutase (SOD, ) is any of a family of enzymes that alternately catalyze the dismutation (or partitioning) of the superoxide () anion radical into normal molecular oxygen (O2) and hydrogen peroxide (). Superoxide is produced as a by-product of oxygen metabolism and, if not regulated, causes many types of cell damage. Hydrogen peroxide is also damaging and is degraded by other enzymes such as catalase. Thus, SOD is an important antioxidant defense in nearly all living cells exposed to oxygen. One exception is Lactobacillus plantarum and related lactobacilli, which use intracellular manganese to prevent damage from reactive .
Chemical reaction SODs catalyze the disproportionation of superoxide: + → + In this way, is converted into two less damaging species.
The general form, applicable to all the different metal−coordinated forms of SOD, can be written as follows: + → + + + → +
The reactions by which SOD−catalyzed dismutation of superoxide for Cu,Zn SOD can be written as follows: + → + (reduction of copper; oxidation of superoxide) + + → + (oxidation of copper; reduction of superoxide)
where M = Cu (n=1); Mn (n=2); Fe (n=2); Ni (n=2) only in prokaryotes.
In a series of such reactions, the oxidation state and the charge of the metal cation oscillates between n and n+1: +1 and +2 for Cu, or +2 and +3 for the other metals.
Types
General
Irwin Fridovich and Joe McCord at Duke University discovered the enzymatic activity of superoxide dismutase in 1968. SODs were previously known as a group of metalloproteins with unknown function; for example, CuZnSOD was known as erythrocuprein (or hemocuprein, or cytocuprein) or as the veterinary anti-inflammatory drug "Orgotein". Likewise, Brewer (1967) identified a protein that later became known as superoxide dismutase as an indophenol oxidase by protein analysis of starch gels using the phenazine-tetrazolium technique.
There are three major families of superoxide dismutase, depending on the protein fold and the metal cofactor: the Cu/Zn type (which binds both copper and zinc), Fe and Mn types (which bind either iron or manganese), and the Ni type (which binds nickel).
Copper and zinc – most commonly used by eukaryotes, including humans. The cytosols of virtually all eukaryotic cells contain a SOD enzyme with copper and zinc (Cu-Zn-SOD). For example, Cu-Zn-SOD available commercially is normally purified from bovine red blood cells. The bovine Cu-Zn enzyme is a homodimer of molecular weight 32,500. It was the first SOD whose atomic-detail crystal structure was solved, in 1975.. It is an 8-stranded "Greek key" beta-barrel, with the active site held between the barrel and two surface loops. The two subunits are tightly joined back-to-back, mostly by hydrophobic and some electrostatic interactions. The ligands of the copper and zinc are six histidine and one aspartate side-chains; one histidine is bound between the two metals. Iron or manganese – used by prokaryotes and protists, and in mitochondria and chloroplasts Iron – Many bacteria contain a form of the enzyme with iron (Fe-SOD); some bacteria contain Fe-SOD, others Mn-SOD, and some (such as E. coli) contain both. Fe-SOD can also be found in the chloroplasts of plants. The 3D structures of the homologous Mn and Fe superoxide dismutases have the same arrangement of alpha-helices, and their active sites contain the same type and arrangement of amino acid side-chains. They are usually dimers, but occasionally tetramers. Manganese – Nearly all mitochondria, and many bacteria, contain a form with manganese (Mn-SOD): For example, the Mn-SOD found in human mitochondria. The ligands of the manganese ions are 3 histidine side-chains, an aspartate side-chain and a water molecule or hydroxy ligand, depending on the Mn oxidation state (respectively II and III).; Nickel – prokaryotic. This has a hexameric (6-copy) structure built from right-handed 4-helix bundles, each containing N-terminal hooks that chelate a Ni ion. The Ni-hook contains the motif His-Cys-X-X-Pro-Cys-Gly-X-Tyr; it provides most of the interactions critical for metal binding and catalysis and is, therefore, a likely diagnostic of NiSODs.;
In higher plants, SOD isozymes have been localized in different cell compartments. Mn-SOD is present in mitochondria and peroxisomes. Fe-SOD has been found mainly in chloroplasts but has also been detected in peroxisomes, and CuZn-SOD has been localized in cytosol, chloroplasts, peroxisomes, and apoplast.
Human
There are three forms of superoxide dismutase present in humans, in all other mammals, and most chordates. SOD1 is located in the cytoplasm, SOD2 in the mitochondria, and SOD3 is extracellular. The first is a dimer (consists of two units), whereas the others are tetramers (four subunits). SOD1 and SOD3 contain copper and zinc, whereas SOD2, the mitochondrial enzyme, has manganese in its reactive centre. The genes are located on chromosomes 21, 6, and 4, respectively (21q22.1, 6q25.3 and 4p15.3-p15.1).
Plants
In higher plants, superoxide dismutase enzymes (SODs) act as antioxidants and protect cellular components from being oxidized by reactive oxygen species (ROS). ROS can form as a result of drought, injury, herbicides and pesticides, ozone, plant metabolic activity, nutrient deficiencies, photoinhibition, temperature above and below ground, toxic metals, and UV or gamma rays. To be specific, molecular O2 is reduced to (a ROS called superoxide) when it absorbs an excited electron released from compounds of the electron transport chain. Superoxide is known to denature enzymes, oxidize lipids, and fragment DNA. SODs catalyze the production of O2 and from superoxide (), which results in less harmful reactants.
When acclimating to increased levels of oxidative stress, SOD concentrations typically increase with the degree of stress conditions. The compartmentalization of different forms of SOD throughout the plant makes them counteract stress very effectively. There are three well-known and -studied classes of SOD metallic coenzymes that exist in plants. First, Fe SODs consist of two species, one homodimer (containing 1–2 g Fe) and one tetramer (containing 2–4 g Fe). They are thought to be the most ancient SOD metalloenzymes and are found within both prokaryotes and eukaryotes. Fe SODs are most abundantly localized inside plant chloroplasts, where they are indigenous. Second, Mn SODs consist of a homodimer and homotetramer species each containing a single Mn(III) atom per subunit. They are found predominantly in mitochondrion and peroxisomes. Third, Cu-Zn SODs have electrical properties very different from those of the other two classes. These are concentrated in the chloroplast, cytosol, and in some cases the extracellular space. Note that Cu-Zn SODs provide less protection than Fe SODs when localized in the chloroplast.
Bacteria
Human white blood cells use enzymes such as NADPH oxidase to generate superoxide and other reactive oxygen species to kill bacteria. During infection, some bacteria (e.g., Burkholderia pseudomallei) therefore produce superoxide dismutase to protect themselves from being killed.
Biochemistry
SOD out-competes damaging reactions of superoxide, thus protecting the cell from superoxide toxicity. The reaction of superoxide with non-radicals is spin-forbidden (this does not mean that the reaction cannot happen, but that it will be much slower). In biological systems, this means that its main reactions are with itself (dismutation) or with another biological radical such as nitric oxide (NO) or with a transition-series metal. The superoxide anion radical () spontaneously dismutes to O2 and hydrogen peroxide () quite rapidly (~105 M−1s−1 at pH 7). SOD is necessary because superoxide reacts with sensitive and critical cellular targets. For example, it reacts with the NO radical, and makes toxic peroxynitrite.
Because the uncatalysed dismutation reaction for superoxide requires two superoxide molecules to react with each other, the dismutation rate is second-order with respect to initial superoxide concentration. Thus, the half-life of superoxide, although very short at high concentrations (e.g., 0.05 seconds at 0.1mM) is actually quite long at low concentrations (e.g., 14 hours at 0.1 nM). In contrast, the reaction of superoxide with SOD is first order with respect to superoxide concentration. Moreover, superoxide dismutase has the largest kcat/KM (an approximation of catalytic efficiency) of any known enzyme (~7 billion M−1s−1), this reaction being limited only by the frequency of collision between itself and superoxide. That is, the reaction rate is "diffusion-limited".
The high efficiency of superoxide dismutase seems necessary: even at the subnanomolar concentrations achieved by the high concentrations of SOD within cells, superoxide inactivates the citric acid cycle enzyme aconitase, can poison energy metabolism, and releases potentially toxic iron. Aconitase is one of several iron-sulfur-containing (de)hydratases in metabolic pathways shown to be inactivated by superoxide.
Evolution The phylogenetic relationships among superoxide dismutases (SODs) are one of many genetic components that have been used to help reconstruct an early timeline of events and predict the evolutionary descent of species, individuals, or genes from a common ancestor over time. Around the period of Earth's transition from anaerobic to aerobic conditions about 2.4 billion years ago (bya), the evolution of SOD enzymes crucially allowed organisms to overcome the effects of oxidative stress following the surge of molecular oxygen (O2) in the atmosphere (Miller 2012). However, evidence suggests that the origination of reactive oxygen species (ROS) took place as early as 4.1 to 3.5 bya (Inupakutika et al. 2016).Inupakutika et al. (2016). The evolution of reactive oxygen species metabolism, Journal of Experimental Botany, 67(21): 5933–5943. https://doi.org/10.1093/jxb/erw382. For the first aerobic organisms, survival depended largely on their ability to defend against ROS. For this reason, it is relevant to understand the environmental constraints that allowed such protective defense enzymes to evolve.
The Great Oxidation Event Atmospheric and oceanic compositions have drastically changed since the formation of early Earth. One significant event, the Great Oxidation Event (GOE), marked the period of time in which oxygen became a major component of Earth's atmosphere and surface ocean. However, the physical or biochemical drivers responsible for the transition from a reducing to oxidizing environment remains up for debate (Olejarz et al. 2021).Olejarz et al. (2021). The Great Oxygenation Event as a consequence of ecological dynamics modulated by planetary change. Nat. Commun., 12: 3985. doi.org/10.1038/s41467-021-23286-7. To date, the evolution of cyanobacteria and cyanobacterial photosynthesis is commonly accepted as the primary driver of oxygen production, alongside several physical events behaving as proximal drivers of environmental state change (Kasting 2013; Inupakutika et al. 2016).Kasting (2013). What caused the rise of atmospheric O2?
Chem. Geo., 362: 13-25. doi.org/10.1016/j.chemgeo.2013.05.039.Inupakutika et al. (2016). The evolution of reactive oxygen species metabolism, Journal of Experimental Botany, 67(21): 5933–5943. https://doi.org/10.1093/jxb/erw382.
Selective Pressure and Enzyme Evolution