Superoxide dismutases: ancient enzymes and new insights

Abstract

Superoxide dismutases (SODs) catalyze the de toxification of superoxide. SODs therefore acquired great importance as O(2) became prevalent following the evolution of oxygenic photosynthesis. Thus the three forms of SOD provide intriguing insights into the evolution of the organisms and organelles that carry them today. Although ancient organisms employed Fe-dependent SODs, oxidation of the environment made Fe less bio-available, and more dangerous. Indeed, modern lineages make greater use of homologous Mn-dependent SODs. Our studies on the Fe-substituted MnSOD of Escherichia coli, as well as redox tuning in the FeSOD of E. coli shed light on how evolution accommodated differences between Fe and Mn that would affect SOD performance, in SOD proteins whose activity is specific to one or other metal ion.

Figure 1

comparison of the ribbon structures that characterize the three families of SOD. In FeSOD and Cu,ZnSOD one monomer is coloured, for NiSOD two monomers are coloured. Each structure in the second row displays the view obtained by rotating the structure above by approximately 90 ° around a horizontal axis in the plane of the page, tipping what was the top of the figure in the upper row towards the back. The NiSODs are homohexamers of four-helix bundles of total molecular weight ≈ 80 kDa [7]. Each four-helix bundle binds a Ni ion (green sphere) at the N-terminus. However each Ni site also derives supporting hydrogen bonds from residues from the neighboring four-helix bundle in a reciprocal arrangement, so two four-helix bundles are colored and the other four are shown in greys. The Cu,ZnSODs are generally 32 kDa homodimers (or dimers of dimers), where each monomer is a flattened eight-strand beta barrel . The Cu and Zn ions (gold and silver spheres, respectively) are bound on the outside of the barrel by two loops, including a short helix. The Fe or MnSODs are 45 kDa homodimers (or dimers thereof) where each monomer includes an alpha-helical N-terminal domain and a C-terminal domain comprised of a three-stranded beta sheet surrounded by alpha helices. The Mn or Fe ion (red sphere) is bound between the two domains by two amino acids from each and a solvent molecule (orange sphere). Cartoons were made using Pymol [8] and the coordinates 1Q0D.pdb for NiSOD [3], 1HL5.pdb chains F and M [7,9] for Cu,ZnSOD, and 1ISB.pdb for FeSOD [10,11].

Figure 2

A: Overlay of the backbones of FeSOD (orange) and Fe-substituted MnSOD (Fe(Mn)SOD), magenta) and B: detail of the active sites of the overlain proteins. Only one monomer is shown. Figure was made using Pymol [8] and the coordinates 1ISB.pdb and 1MMM.pdb respectively [10,12]. The amino acid numbering of E. coli FeSOD and MnSOD are used throughout.

Figure 3

cartoon of redox tuning of the Fe^3+/2+ and Mn^3+/2+ ions by the (Fe)SOD and (Mn)SOD proteins (the proteins of FeSOD and MnSOD, respectively).

Figure 4

Distribution of SODs in cells and branches of life. Different colours indicate the different SODs: orange for FeSOD, magenta for MnSOD, blue for Cu,ZnSOD and green for NiSOD. Quaternary states of SODs are indicated in the cell cartoon but not in the tree. This cartoon summarizes general features only, for details please see the text and references [46-48]. There is an older report of CuSOD in the nucleus .

Scheme 1

Proton-coupled reduction of the metal ion of SODs, where M stands for Fe or Mn, and the Gln H-bonding to the coordinated solvent is Gln69 of FeSOD or Gln146 of MnSOD (see Figure 2B). Details of the coordination are omitted from the right-hand side for the sake of clarity, since they do not change.