Iron sulfur clusters

Iron-sulfur proteins play important roles in electron transfer and catalysis in organisms ranging from simple bacteria through to higher animals. The common structural motif is iron tetrahedrally coordinated by sulfur donors with the single metal centre in rubredoxin bound by four cysteine thiolates while the 2Fe and 4Fe sites of ferredoxins have respectively two and one monodentate thiolate ligands and two or three bridging sulfido units (Fig. 11). 

The relatively weak tetrahedral ligand field ensures that the Fe centres remain high spin in both the -1-3 and +2 oxidation states. This has an important consequence since the number of unpaired electrons, and hence spin polarisation, is high. 

In a spin unrestricted treatment where the up-spin electrons are allowed to have different spatial properties to their down-spin counterparts, the extra exchange stabilisation of the majority spin (say, up-spin), means that their energies are lowered. Since in metal complexes, the spin is located 

The broken symmetry wavefunction is not itself a pure spin state. However, spin projection techniques allow the approximate energies and properties of the correct spin states to be calculated. 

To successfully describe the structure and function of nitrogenase, it is important to understand the behavior of the metal-sulfur clusters that are a vital part of this complex enzyme. Metal-sulfur clusters are many, varied, and usually involved in redox processes carried out by the protein in which they constitute prosthetic centers. They may be characterized by the number of iron ions in the prosthetic center that is, rubredoxin (Rd) contains one Fe ion, ferredoxins (Fd) contain two or four Fe ions, and aconitase contains three Fe ions.7 In reference 18, Lippard and Berg present a more detailed description of iron-sulfur clusters only the [Fe4S4] cluster typical of that found in nitrogenase s Fe-protein is discussed in some detail here. The P-cluster and M center of MoFe-protein, which are more complex metal-sulfur complexes, are discussed in Sections 6.5.2. and 6.5.3. 

The fourth state with [Fe4S4]° shown in Table 6.1 was recently described as the most reduced form possible for the Fe-protein s [Fe4S4] cluster.16 Usually, only two oxidation states for a given metal-sulfur cluster are stable. Therefore a stable [Fe4S4]° state in Fe-protein s iron-sulfur cluster (as appears likely from experimental evidence presented in reference 16) would be unique because the cluster would then have three stable oxidation states, [Fe4S4]2+/1+/0. It appears also that the all-ferrous state is only stable in the protein-bound cluster and not for model 

Oxidation State Formal Valence EPR g Values (Temperature) Mossbauer Isomer Shift, 8 (mm/s) Cx (nm), (Extinction Coefficient, xl0 3, per Fe) 

Iron-sulfur clusters have been self-assembled by chemists since the 1980s according to the following reactions.17 This work has continued to the present time as discussed below in Section 6.6. 

Core extrusion studies—removal of the iron-sulfur cluster intact from the enzyme surroundings—have been carried out and the iron-cluster types in proteins identified through the process shown in equation 6.10.18 DMS0/H20 is the protein unfolding solvent for this process. By this method, Fe-protein and MoFe-protein metal-sulfur clusters have been removed from the holoenzyme for separate analysis by many instrumental techniques. 

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A substantial fraction of the named enzymes are oxido-reductases, responsible for shuttling electrons along metabolic pathways that reduce carbon dioxide to sugar (in the case of plants), or reduce oxygen to water (in the case of mammals). The oxido-reductases that drive these processes involve a small set of redox active cofactors , that is, small chemical groups that gain or lose electrons. These cofactors include iron porjDhyrins, iron-sulfur clusters and copper complexes as well as organic species that are ET active. 

Iron Sulfur Compounds. Many molecular compounds (18—20) are known in which iron is tetrahedraHy coordinated by a combination of thiolate and sulfide donors. Of the 10 or more stmcturaHy characterized classes of Fe—S compounds, the four shown in Figure 1 are known to occur in proteins. The mononuclear iron site REPLACE occurs in the one-iron bacterial electron-transfer protein mbredoxin. The [2Fe—2S] (10) and [4Fe—4S] (12) cubane stmctures are found in the 2-, 4-, and 8-iron ferredoxins, which are also electron-transfer proteins. The [3Fe—4S] voided cubane stmcture (11) has been found in some ferredoxins and in the inactive form of aconitase, the enzyme which catalyzes the stereospecific hydration—rehydration of citrate to isocitrate in the Krebs cycle. In addition, enzymes are known that contain either other types of iron sulfur clusters or iron sulfur clusters that include other metals. Examples include nitrogenase, which reduces N2 to NH at a MoFe Sg homocitrate cluster carbon monoxide dehydrogenase, which assembles acetyl-coenzyme A (acetyl-CoA) at a FeNiS site and hydrogenases, which catalyze the reversible reduction of protons to hydrogen gas. 

J-M Mouesca, JL Chen, F Noodleman, D Bashford, DA Case. Density functional/Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters. J Am Chem Soc 116 11898-11914, 1994. 

R Langen, GM Jensen, U Jacob, PJ Stephens, A Warshel. Protein control of iron-sulfur cluster redox potentials. J Biol Chem 267 25625-25627, 1992. 

PS Brereton, FJM Verhagen, ZH Zhou, MWW Adams. Effect of iron-sulfur cluster environment m modulating the thermodynamic properties and biological function of ferredoxm from Pyrococcus furiosus. Biochemistry 37 7351-7362, 1998. 

Nonrepetitive but well-defined structures of this type form many important features of enzyme active sites. In some cases, a particular arrangement of coil structure providing a specific type of functional site recurs in several functionally related proteins. The peptide loop that binds iron-sulfur clusters in both ferredoxin and high potential iron protein is one example. Another is the central loop portion of the E—F hand structure that binds a calcium ion in several calcium-binding proteins, including calmodulin, carp parvalbumin, troponin C, and the intestinal calcium-binding protein. This loop, shown in Figure 6.26, connects two short a-helices. The calcium ion nestles into the pocket formed by this structure. 

FIGURE 20.7 (a) The aconitase reaction converts citrate to cis-aconitate and then to isocitrate. Aconitase is stereospecific and removes the pro-/ hydrogen from the pro-/ arm of citrate, (b) The active site of aconitase. The iron-sulfur cluster (red) is coordinated by cysteines (yellow) and isocitrate (white). 

Inspection of the citrate structure shows a total of four chemically equivalent hydrogens, but only one of these—the pro-/J H atom of the pro-i arm of citrate—is abstracted by aeonitase, which is quite stereospecific. Formation of the double bond of aconitate following proton abstraction requires departure of hydroxide ion from the C-3 position. Hydroxide is a relatively poor leaving group, and its departure is facilitated in the aeonitase reaction by coordination with an iron atom in an iron-sulfur cluster. 

The final step of the reaction involves the transfer of two electrons from iron-sulfur clusters to coenzyme Q. Coenzyme Q is a mobile electron carrier. Its isoprenoid tail makes it highly hydrophobic, and it diffuses freely in the hydrophobic core of the inner mitochondrial membrane. As a result, it shuttles electrons from Complexes I and II to Complex III. The redox cycle of UQ is shown in Figure 21.5, and the overall scheme is shown schematically in Figure 21.6. 

When induced in macrophages, iNOS produces large amounts of NO which represents a major cytotoxic principle of those cells. Due to its affinity to protein-bound iron, NO can inhibit a number of key enzymes that contain iron in their catalytic centers. These include ribonucleotide reductase (rate-limiting in DNA replication), iron-sulfur cluster-dependent enzymes (complex I and II) involved in mitochondrial electron transport and cis-aconitase in the citric acid cycle. In addition, higher concentrations of NO,... 

In summary, it appears that the protein has to adopt the correct fold before the Rieske cluster can be inserted. The correct folding will depend on the stability of the protein the Rieske protein from the thermoacidophilic archaebacterium Sulfolobus seems to be more stable than Rieske proteins from other bacteria so that the Rieske cluster can be inserted into the soluble form of the protein during expression with the help of the chaperonins. If the protein cannot adopt the correct fold, the result will be either no cluster or a distorted iron sulfur cluster, perhaps using the two cysteines that form the disulfide bridge in correctly assembled Rieske proteins. 

Probably involved with NifS in iron-sulfur cluster synthesis Possibly accelerate MoFe protein maturation Unknown function... 

Plus 241 distance constraints for the unassigned residues close to the iron—sulfur cluster derived from the X-ray structure... 

Ragsdale, S. W. Kumar, M. Zhao, S. Menon, S. Seravalli, J. Doukov, T. Discovery of a Bio-organometallic Reaction Sequence Involving Vitamin B12 and Nickel/ Iron-Sulfur Clusters Wiley-VCH Weinheim, Germany, 1998. 

During the 1960s, research on proteins containing iron—sulfur clusters was closely related to the field of photosynthesis. Whereas the first ferredoxin, a 2[4Fe-4S] protein, was obtained in 1962 from the nonphotosynthetic bacterium Clostridium pasteurianum (1), in the same year, a plant-type [2Fe-2S] ferredoxin was isolated from spinach chloroplasts (2). Despite the fact that members of this latter class of protein have been reported for eubacteria and even archaebacteria (for a review, see Ref. (3)), the name plant-type ferredoxin is often used to denote this family of iron—sulfur proteins. The two decades... 

In 1987, the iron-sulfur clusters Fa and Fb acting as terminal electron acceptors in photosystem I have been shown to be located on a... 

Cluster Fx was also identified via its EPR spectral features in the RCI photosystem from green sulfur bacteria 31, 32) and the cluster binding motif was subsequently found in the gene sequence 34 ) of the (single) subunit of the homodimeric reaction center core (for a review, see 54, 55)). Whereas the same sequence motif is present in the RCI from heliobacteria (50), no EPR evidence for the presence of an iron-sulfur cluster related to Fx has been obtained. There are, however, indications from time-resolved optical spectroscopy for the involvement of an Fx-type center in electron transfer through the heliobacterial RC 56). 

Studies (see, e.g., (101)) indicate that photosynthesis originated after the development of respiratory electron transfer pathways (99, 143). The photosynthetic reaction center, in this scenario, would have been created in order to enhance the efficiency of the already existing electron transport chains, that is, by adding a light-driven cycle around the cytochrome be complex. The Rieske protein as the key subunit in cytochrome be complexes would in this picture have contributed the first iron-sulfur center involved in photosynthetic mechanisms (since on the basis of the present data, it seems likely to us that the first photosynthetic RC resembled RCII, i.e., was devoid of iron—sulfur clusters). 

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