Iron-sulfur enzymes

Iron-sulfur clusters (7) occur as prosthetic groups in oxidoreductases, but they are also found in lyases—e.g., aconitase (see p. 136) and other enzymes. Iron-sulfur clusters consist of 2-4 iron ions that are coordinated with cysteine residues of the protein (-SR) and with anorganic sulfide ions (S). Structures of this type are only stable in the interior of proteins. Depending on the number of iron and sulfide ions, distinctions are made between [Fe2S2], [Fe3S4], and [Fe4S4] clusters. These structures are particularly numerous in the respiratory chain (see p. 140), and they are found in all complexes except complex IV. 

DET has been observed for the following active sites of redox proteins or redox enzymes iron-sulfur clusters (2Fe-2S, 3Fe-4S, 4Fe-4S,... 

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. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

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. 

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,... 

CODH/ACS is an extremely oxygen-sensitive protein that has been found in anaerobic microbes. It also is one of the three known nickel iron-sulfur proteins. Some authors would consider that there are only two, since the CODH and ACS activities are tightly linked in many organisms. However, there is strong evidence that the ACS and CODH activities are associated with different protein subunits and the reactions that the two enzymes catalyze are quite different. CODH catalyzes a redox reaction and ACS catalyzes the nonredox condensation of a methyl group, a carbonyl group, and an organic thiol (coenzyme A). 

This key enzyme of the dissimilatory sulfate reduction was isolated from all Desulfovibrio strains studied until now 135), and from some sulfur oxidizing bacteria and thermophilic Archaea 136, 137). The enzymes isolated from sulfate-reducing bacteria contain two [4Fe-4S] clusters and a flavin group (FAD) as demonstrated by visible, EPR, and Mossbauer spectroscopies. With a total molecular mass ranging from 150 to 220 kDa, APS reductases have a subunit composition of the type 012)32 or 02)3. The subunit molecular mass is approximately 70 and 20 kDa for the a and )3 subunits, respectively. Amino-acid sequence data suggest that both iron-sulfur clusters are located in the (3 subunit... 

These enzymes may contain other redox-active sites (iron-sulfur centers, hemes, and/or flavins), either in distinct domains of a single polypeptide or bound in separate subunits. These additional cofactors perform electron transfer from the molybdenum center to an external electron acceptor/donor. 

An important advance on these studies was the possibility of isolating AORs from Fe enriched media with obvious interest for an iron-sulfur center site labeling, with enhanced sensitivity of the Mossbauer studies. The work developed with bacterial systems is advantageous as compared with mammalian systems for isotopic labeling and opens the possibility of a direct measurement of substrate binding. Spectra of the enzyme in oxidized, partially reduced, benzaldehyde-reacted, and fully reduced states were recorded at different temperatures and with variable externally applied magnetic fields (222). In the oxidized enzyme, the clusters are diamag-... 

Formate dehydrogenases are a diverse group of enzymes found in both prokaryotes and eukaryotes, capable of converting formate to CO2. Formate dehydrogenases from anaerobic microorganisms are, in most cases, Mo- or W- containing iron-sulfur proteins and additionally flavin or hemes. Selenium cysteine is a Mo- ligand. 

D. desulfuricans is able to grow on nitrate, inducing two enzymes that responsible for the steps of conversion of nitrate to nitrite (nitrate reductase-NAP), which is an iron-sulfur Mo-containing enzyme, and that for conversion of nitrite to ammonia (nitrite reduc-tase-NIR), which is a heme-containing enzyme. Nitrate reductase from D. desulfuricans is the only characterized enzyme isolated from a sulfate reducer that has this function. The enzyme is a monomer of 74 kDa and contains two MGD bound to a molybdenum and one [4Fe-4S] center (228, 229) in a single polypeptide chain of 753 amino acids. FXAFS data on the native nitrate reductase show that besides the two pterins coordinated to the molybdenum, there is a cysteine and a nonsulfur ligand, probably a Mo-OH (G. N. George, personal communication). 

Similar difficulties have been encountered in the case of complex enzymes such as fumarate reductase and nitrate reductase from E. coli, in which substituting certain Cys ligands led to the loss of several if not all the iron-sulfur centers (171, 172). However, in the case of nitrate reductase, which possesses one [3Fe-4S] and three [4Fe-4S] centers, it was possible to remove selectively one [4Fe-4S]... 

The redox potentials of iron-sulfur centers vary considerably, depending on the type of center (242) and its environment in the protein (243), ranging from about -700 mV in the case of some [4Fe-4S] centers (244, 245) to about +450 mV in the case of some [4Fe-4S] centers (246). Iron-sulfur centers therefore act as redox centers in numerous electron transfer systems, including the respiratory and photo synthetic bioenergetic chains as well as a wide variety of redox enzymes. Among the many studies that have dealt with these systems, some have yielded structural information of the kind described in Section III. Most of them were designed, however, to measure the... 

Iron-sulfur centers can participate in regulation mechanisms either directly, when they control the activity of an enzyme, or at a more integrated level, when they modulate the expression of some genes. The regulation mechanisms that have been elucidated so far involve either a change in the redox state or the interconversion of iron—sulfur centers. 

A relationship between the redox state of an iron—sulfur center and the conformation of the host protein was furthermore established in an X-ray crystal study on center P in Azotobacter vinelandii nitroge-nase (270). In this enzyme, the two-electron oxidation of center P was found to be accompanied by a significant displacement of about 1 A of two iron atoms. In both cases, this displacement was associated with an additional ligation provided by a serine residue and the amide nitrogen of a cysteine residue, respectively. Since these two residues are protonable, it has been suggested that this structural change might help to synchronize the transfer of electrons and protons to the Fe-Mo cofactor of the enzyme (270). 

Aconitase An Iron-Sulfur Enzyme Mary Claire Kennedy and C. David Stout... 

H)2-D3 is a weak agonist and must be modified by hydroxylation at position Cj for full biologic activity. This is accomplished in mitochondria of the renal proximal convoluted tubule by a three-component monooxygenase reaction that requires NADPFl, Mg, molecular oxygen, and at least three enzymes (1) a flavoprotein, renal ferredoxin reductase (2) an iron sulfur protein, renal ferredoxin and (3) cytochrome P450. This system produces l,25(OH)2-D3, which is the most potent namrally occurring metabolite of vitamin D. 

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