Aconitase iron coordination

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. 

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). 

Fig. 6. A schematic view of the [3Fe-4S] Emd [4Fe-4S] cores, as versatile structures. The absence of one site leads to the formation of a [3Fe-4S] core. The cubane structure can incorporate different metals (in proteins, M = Fe, Co, Zn, Cd, Ni, Tl, Cs), and S, N, O may be coordinating atoms from hgands (Li). The versatihty csm be extended to higher coordination number at the iron site and a water molecule can even be a ligand, exchangeable with substrate (as in the case of aconitase (,87)). The most characteristic binding motifs are schematically indicated, for different situations proteins accommodating [3Fe-4S], [4Fe-4S], [3Fe-4S] + [4Fe-4S], and [4Fe-4S] -I- [4Fe-4S] clusters. A disulfide bridge may replace a cluster site (see text).

Figure 7.8 Regulation of IRP-1 and IRP-2. The two IRPs are shown as homologous four domain proteins that bind to IREs (left) In iron-replete cells, IRP-1 assembles a cubane Fe-S cluster that is liganded via cys-437, -503 and -506. Similar cysteines are conserved in IRP-2 (Cys-512, -578 and -581), but it is unresolved as to whether they also coordinate an Fe-S cluster, (right) In iron-replete cells, IRP-2 is targeted for destruction via a specific region (shaded in black), whereas IRP-1, with a 4Fe-4S cluster, is stable and active as a cytoplasmic aconitase. Multiple signals induce IRE-binding by IRP-1 with distinct kinetics. Whether or not NO and H2O2 induce IRP-1 by apoprotein formation remains to be addressed directly. From Hentze and Kuhn, 1996. Copyright (1996) National Academy of Sciences, USA.

Figure 13.17 Role of clusters in substrate binding—in aconitase the cluster geometry shifts from 4- to 6-coordination on substrate binding. The coordinating iron atom abstracts the hydroxide anion during dehydration. (From Imlay, 2006. Reproduced with permission of Blackwell Publishing Ltd.)...

Early attempts to purify the enzyme brought the quick realization that aconitase is easily inactivated (6,7). In the early 1950 s Dickman and Qoutier (8,9) found that inactivated aconitase could be reactivated by incubation with iron and a reduc-tant. From kinetic analyses of the iron and reductant effects on enzyme activity, Morrison argued that both formed Michaelis-Menten complexes wiA the enzyme (10). This refuted the earlier idea that the sole role of the reductant was to maintain iron in a reduced state (9). Of several metal cations tried, only ferrous ion was found to be capable of this reactivation process (8,11). Because of the absolute requirement for iron in activation, the known chelation properties of citrate, and Ogston s 3-point attachment proposal, Speyer and Dickman proposed that the active site iron provides three coordination sites for substrate binding - one for hydroxyl and two for carboxyl groups (12). 

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. 

A brief historical note on the structure of the iron-sulfur clusters in ferredoxins is relevant. After the first analytical results revealed the presence of (nearly) equimolar iron and acid-labile sulfur, it was clear that the metal center in ferredoxins did not resemble any previously characterized cofactor type. The early proposals for the Fe S center structure were based on a linear chain of iron atoms coordinated by bridging cysteines and inorganic sulfur (Blomstrom et al., 1964 Rabino-witz, 1971). While the later crystallographic analyses of HiPIP, PaFd, and model compounds (Herskovitz et al., 1972) demonstrated the cubane-type structure of the 4Fe 4S cluster, the original proposals have turned out to be somewhat prophetic. Linear chains of sulfide-linked irons are observed in 2Fe 2S ferredoxins and in the high-pH form of aconitase. Cysteines linked to several metal atoms are present in metallothionein. The chemistry of iron-sulfur clusters is rich and varied, and undoubtedly many other surprises await in the future. 

It is now clear that in addition to their widespread involvement in electron transfer pathways, iron-sulfur clusters function as catalytic centers in a wide variety of enzymes. The first example of such an enzyme is aconitase. It was at first thought that the role of the iron-sulfur group was regulatory, but it is now clear that in this enzyme the iron-sulfur group is part of the catalytic site. One of the iron atoms can coordinate water or hydroxyl and plays a key role in the isomerization catalyzed by the enzyme (Emptage et al., 1983). 

If this mechanism is correct, the aconitase reaction is an excellent illustration of the influence of the stereochemistry of the metal, as well as its charge, upon the course of a biochemical reaction. The charge on the iron is, of course, responsible for the formation of the resonating carbonium ions A and B from C, D, or E. In C and D the flow of electrons toward iron severs the bond between carbon and the hydroxyl group, whereas in E the proton is released from coordinated water and attached to one of the two ethylenic carbon atoms. The stereochemistry of the iron atom can be credited with holding the organic molecule and the hydroxide in their proper spatial relationship in A and B. It has been recently demonstrated that the complexes of the aconitase substrates with nickel have the structures postulated by Speyer and Dickman and shown in Figure 3 (19). 

Numerous cellular enzymes and coenzymes require iron, either as an integral part of the molecule or as a cofactor. Notable are the peroxidases and cytochromes, all of which, like Hb, are heme proteins. Other enzymes, such as aconitase and ferredoxin, have iron that is coordinated with sulfur in a so-called iron-sulfiir cluster. Nearly half of the enzymes of the Krehs cycle contain iron. These enzymes and coenzymes, which appear in aU nucleated cells of the body, are referred to collectively as the tissue iron compartment. The tissue iron compartment normally amounts to approximately 8 mg. Although a small compartment, it is metabolicaUy critical. Some iron enzyme activities dimmish early in the course of iron deficiency. ... 

Amico. P., Daniele, P. G., Cucinotta, V., Rizzarelli, E., and Sammartano, S. (1979). Equilibrium study of iron(n) and manganese(II) complexes with citrate ion in aqueous solution relevance to coordination of citrate to the active site of aconitase and to gastrointestinal absorption of some essential metal ions. Inorg. Chim. Acta 36, 1-7. 

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