Aconitase geometry

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). 

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.)...

Why did nature use an Fe-S cluster to catalyze this reaction, when an enzyme such as fumarase can catalyze the same type of chemistry in the absence of any metals or other cofactors One speculation would be that since aconitase must catalyze both hydrations and dehydrations, and bind substrate in two orientations, Fe in the comer of a cubane cluster may provide the proper coordination geometry and electronics to do all of these reactions. Another possibility is that the cluster interconversion is utilized in vivo to regulate enzyme activity, and thus, help control cellular levels of citrate. A third, but less likely, explanation is that during evolution an ancestral Fe-S protein, whose primary function was electron transfer, gained the ability to catalyze the aconitase reaction through random mutation. 

Aconitase was initially crystallized in the [3Fe-4S]" " form, and these crystals could be converted to the [4Fe S] " " form by addition of ferrous ammonium sulfate. Alternatively, anaerobic crystallization methods were used to crystallize the [4Fe-4S] " " form directly." The iron-sulfur cluster of aconitase sits within a solvent-filled cleft in the protein structure and is coordinated by Cys 358, Cys 421, and Cys 424. The [3Fe S]+ cluster shows the typically cuboidal geometry, with the open iron site directed toward the active site cleft. Conversion to the active [4Fe-4S] " " form results in almost no structural perturbation, with the extra iron atom simply being inserted into the vacant site in the cluster. The fourth iron is tetrahedrally coordinated, but with a solvent hydroxide rather than a cysteine as the fourth ligand. (The electron density clearly reveals a bound solvent, and previous ENDOR studies had demonstrated that the bound species was associated with only a single proton.)... 

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