Superoxide dismutase structure, active site

Fig. 7. A Structural representation of Cu-Zn superoxide dismutase (SOD) active site (from Ref. 31c). B X-band (left) (77K v = 9.2 GHz) (from Ref. 25) and Q-band (right) (173 K v = 35 GHz) (from Ref. 26) EPR spectra of bovine Cu-Zn SOD. C Optical absorption spectra of native...

Wuerges J, J-W Lee, Y-I Yim, H-S Yrm, S-O Kang, KD Carugo (2004) Crystal structure of nickel-containing superoxide dismutase reveals another type of active site. Proc Natl Acad Sci USA 101 8569-8574. 

Nickel is found in thiolate/sulflde environment in the [NiFe]-hydrogenases and in CODH/ACS.33 In addition, either a mononuclear Ni-thiolate site or a dinuclear cysteine-S bridged structure are assumed plausible for the new class of Ni-containing superoxide dismutases, NiSOD (A).34 [NiFe]-hydrogenase catalyzes the two-electron redox chemistry of dihydrogen. Several crystal structures of [NiFe]-hydrogenases have demonstrated that the active site of the enzyme consists of a heterodinuclear Ni—Fe unit bound to thiolate sulfurs of cysteine residues with a Ni—Fe distance below 3 A (4) 35-39 This heterodinuclear active site has been the target of extensive model studies, which are summarized in Section 6.3.4.12.5. 

Imidazoles are of interest as bridging ligands particularly with regard to mimics of the active site of Cu-Zn superoxide dismutase (SOD). Structures with imidazolate bridges have been... 

Carloni, P., P. E. Blochl, and M. Parrinello. 1995. Electronic Structure of the Cu, Zn Superoxide Dismutase Active Site and Its Interactions with the Substrate. J. Phys. Chem. 99, 1338. 

One last class of mononuclear non-haem iron enzyme that we have not yet considered, consists of the microbial superoxide dismutases with Fe(III) at their active site. The crystal structure of the E. coli enzyme shows a coordination geometry reminiscent of protocatechuate 3,4-dioxygenase, with four endogenous protein ligands, three His and one Asp residue, and one bound water molecule (Carlioz et ah, 1988). 

Carloni, P., Blochl, P. E. and Parrinello, M. Electronic structure of the Cu,Zn superoxide dismutase active site and its interactions with the substrate, J.Phys.Chem., 99 (1995), 1338-1348... 

It was clear for some time that a number of zinc enzymes required two or more metal ions for full activity, but in the absence of X-ray structural data the location of these metal centres with regard to one another was often uncertain. When the first 3-D structures began to appear, it became clear that the metals were in close proximity. A particular feature of many of these enzymes was the presence of a bridging ligand between two of the metal sites, usually an Asp residue of the protein, which is occasionally replaced by a water molecule. While some of the sites contain only Zn ions, several contain Zn in combination with Cu (in cytosolic superoxide dismutases) Fe (in purple acid phosphatases) or Mg (in alkaline phosphatase and the aminopeptidase of lens). 

LoU, B., Kern, J., Saenger, W., Zouni, A. and Biesiadka, J. (2005) Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature, 438, 1040-1044. Miller, A.-F. (2004) Superoxide dismutases active sites that save, but a protein that kills, Curr. Opin. Chem. Biol., 8, 162-168. 

These systems are also described as normal copper proteins due to their conventional ESR features. In the oxidized state, their color is light blue (almost undetectable) due to weak d-d transitions of the single Cu ion. The coordination sphere around Cu, which has either square planar or distorted tetrahedral geometry, contains four ligands with N and/or 0 donor atoms [ 12, 22]. Representative examples of proteins with this active site structure (see Fig. 1) and their respective catalytic function include galactose oxidase (1) (oxidation of primary alcohols) [23,24], phenylalanine hydroxylase (hydroxy-lation of aromatic substrates) [25,26], dopamine- 6-hydroxylase (C-Hbond activation of benzylic substrates) [27] and CuZn superoxide dismutase (disproportionation of 02 superoxide anion) [28,29]. 

Although zinc itself is not redox-active, some class I enzymes containing zinc in their active sites are known. The most prominent are probably alcohol dehydrogenase and copper-zinc superoxide dismutase (Cu,Zn-SOD). AU have in common that the redox-active agent is another transition-metal ion (copper in Cu,Zn-SOD) or a cofactor such as nicotinamide adenine dinucleotide (NAD+/NADH). The Zn(II) ion affects the redox reaction only in an indirect manner, but is nevCTtheless essential and cannot be regarded simply as a structural factor. 

Figure 16-22 (A) Structure of the active site of iron superoxide dismutase from E. coli. From Carlioz et al m Courtesy of M. Ludwig. (B) Interpretive drawing illustrating the single-electron transfer from a superoxide molecule to the Fe3+ of superoxide dismutase and associated proton uptake. Based on Lah et al.376...

Fig. 6.2. Schematic structure of the active site of copper-zinc superoxide dismutase [72]. The zinc ion can be substituted, among others, by copper(II), cobalt(II) and nickel(II) ions.

Fig. 7.4. Schematic structure of the active site of Cu2Zn2-superoxide dismutase. The labels refer to the proton signal assignment for the Cu2Co2 derivative reported in Table 7.3 [15,16].

The most common metal encountered in electron transfer systems is iron, although copper and manganese play vital functions. Merely to emphasise the complexity of the catalysts that are used in biology, the structures of the active sites of ascorbate oxidase (Fig. 10-11) and superoxide dismutase (Fig. 10-12) are presented. It is clear that we have only just begun to understand the exact ways in which metal ions are used to control the reactivity of small molecules in biological systems. 

We have already seen a number of models for the zinc(II) containing enzymes such as carbonic anhydrase in Section 11.3.2. Zinc is an essential component in biochemistry, and forms part of the active site of more then 100 enzymes, of which hydrolases (such as alkaline phosphatase and carboxypeptidase A), transferases (e.g. DNA and RNA polymerase), oxidoreductases (e.g. alcohol dehydrogenase and superoxide dismutase) and lysases (carbonic anhydrase) are the most common. In addition, the non-enzyme zinc finger proteins have an important regulatory function. In many of these systems, the non-redox-active Zn2+ ion is present as a Fewis acidic centre at which substrates are coordinated, polarised and hence activated. Other roles of zinc include acting as a template and playing a structural or regulatory role. 

The structure and enzyme kinetics of bovine erythrocyte superoxide dismutase are reviewed. The protein has a novel imidazolate-bridged copper(II)-zinc(II) catalytic center in each of two identical subunits. Since a C /Cu1 redox couple is responsible for the dismutase activity of the enzyme, the role of zinc is of interest. Both 220-MHz NMR measurements of the exchangeable histidine protons and chemical modifications using diethylpyrocarbonate demonstrate that zinc alone can fold the protein chain in the region of the active site into a conformation resembling that of the native enzyme. Other possible roles for zinc are discussed. Synthetic, magnetic, and structural studies of soluble, imidazolate-bridged copper complexes of relevance to the 4 Cu(II) form of the enzyme have been made. 

Figure 3. The active site of Mn superoxide dismutase on the basis of the X-ray structure of Ludwig et al. (59). The W represents a water-derived ligand, either OH or H20.

---