Aconitase structure

The [3Fe-4S] core is now considered an unique basic iron-sulfur core whose structure was determined in D. gigas Fdll 56, 84) (as well as in aconitase 85-87) and A. vinelandii Fd (57, 59, 80)). The cluster in these proteins have Fe-Fe and Fe-S distances around 2.8 and 2.2 A and the core described as a cuboidal geometry with one comer missing (Fe S stoichiometry of 3 4). 

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).

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 X-ray structures of other aconitases have appeared in the literature. Recently, the crystal structure of human iron regulatory protein, IRPl, in its aconitase form, has been published. Iron regulatory proteins (IRPs) control the translation of proteins involved in iron uptake, storage, and utilization by binding to specific noncoding sequences of the corresponding mRNAs known... 

A third type of trinuclear cluster duplicates the Fe3S stoichiometry that is most accepted for protein-bound 3Fe clusters and in fact appears to be a structural isomer of the 3Fe cluster present in aconitase at least. The [Fe3S (SR) ]ion (3) is obtained by reaction of [Fe(SR) ] " with 1.4 equivalents of sulfur in MeCN, as indicated above (13, 16). It contains a central Fe(III) ligated tetrahedrally by four sulfides that connect it to two terminal Fe(IIl)(SR)2 units. The spectroscopic and magnetic properties of 3 are virtually identical with those of the 3Fe form of aconitase at high pH, but substantially different from those of aconitase under normal physiological conditions (23). Possible structures for the latter that are consistent with available data are shown in Figure 7. 

Furthennore, resonance Raman studies of aconitase by Johnson et al. (53) demonstrated homologous spectra for both inactive and active aconitase. This suggests similar vibrational modes and thus similar core structures for the two forms. Finally, a cubane structure for the [3Fe-4S] cluster is supported by recent protein crystallographic studies of inactive aconitase by Robbins and Stout (54). (Recent results from Jensen s group (55) on the redetermination of the crystal structure of the Azotobacter ferredoxin I clearly show that the 3Fe cluster does not have a [3Fe-3S] ring structure, as originally determined (37), but has a [3Fe-4S] cubane structure.)... 

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 representative sampling of non-heme iron proteins is presented in Fig. 3. Evident from this atlas is the diversity of structural folds exhibited by non-heme iron proteins it may be safely concluded that there is no unique structural motif associated with non-heme iron proteins in general, or even for specific types of non-heme iron centers. Protein folds may be generally classified into several categories (i.e., all a, parallel a/)3, or antiparallel /8) on the basis of the types and interactions of secondary structures (a helix and sheet) present (Richardson, 1981). Non-heme iron proteins are found in all three classes (all a myohemerythrin, ribonucleotide reductase, and photosynthetic reaction center parallel a/)8 iron superoxide dismutase, lactoferrin, and aconitase antiparallel )3 protocatechuate dioxygenase, rubredoxins, and ferredoxins). This structural diversity is another reflection of the wide variety of functional roles exhibited by non-heme iron centers. 

Perhaps one of the most elegant object lessons demonstrating the importance of careful compositional analysis comes from the work by Beinert et al. (1983) on the 3Fe cluster. Even with structural analysis by numerous sophisticated spectroscopic methods and by X-ray diffraction, there was substantial controversy about whether the cluster was a modified cubane structure with four inorganic sulfurs and three ligands or a more open chair structure with three sulfurs and six ligands. The analysis of aconitase indicated four sulfurs and resolved the question in favor of the modified cubane. Further X-ray diffraction studies confirmed the cubane 3Fe 4S cluster for aconitase and ferredoxins from A. vinelandii and Desulfovibrio pgas (Stout et al., 1988 Stout 1988 Kissinger et al., 1989). 

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. 

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