Enzyme coordination geometry

Zn -PDF, 37 pM versus E. coli Fe -PDF), it was successfully used to provide co-crystals bound in the active site of both Co - and Zn -E. coli PDF [58], These structures reveal that the H-phosphonate binds to the metal in a monodentate fashion, adopting a tetrahedral coordination state similar to that of the native resting state of the enzyme. This is in contrast to later co-crystal structures obtained with more potent hydroxamic acid or reverse hydroxamate inhibitors, which bind to the metal in a bidentate fashion vide infra). Presumably these bidentate inhibitors mimic the true transition state of the enzyme, in which the metal centre slips to a penta-coordinate geometry in order to activate the Wformyl carbonyl of the substrate [56, 67]. 

One last class of mononuclear non-haem iron enzyme that we have not yet considered, consists of the microbial superoxide dismutases with Fe(III) at their active site. The crystal structure of the E. coli enzyme shows a coordination geometry reminiscent of protocatechuate 3,4-dioxygenase, with four endogenous protein ligands, three His and one Asp residue, and one bound water molecule (Carlioz et ah, 1988). 

The intriguing question is how the seven-coordinate geometry around the metal center favors its remarkable catalytic activity, knowing that in the native MnSOD and FeSOD enzymes the active metal center has a five-coordinate geometry (3a,14f30). All SOD... 

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. 

Locating minima is not always straightforward since a reaction surface is usually complex, and a geometry optimization calculation will only locate minima close to the starting point. It is usually not feasible to systematically explore all possible conformers, so chemical intuition and corroborative evidence from experiment play important roles. A nice example is the identification of the coordination geometry of oxo-iron(IV) intermediate in TauD (22). As mentioned above, during optimization of enzyme active sites, key atoms are sometimes fixed to mimic the constraints that the protein environment exerts on the active site (20). 

The inhibitors are generally monoanions or neutral molecules capable of deprotonation to yield anionic species. These neutral inhibitors (mostly sulfonamides) (189) bind to the active site Zn-H O. Monovalent anions like I-, CN-, SCN-, N3, NCO-, SH- etc. (190,191), inhibit the catalyzed reaction of CA enzyme by binding directly to the metal ion either by displacing H2O to yield a tetra-coordinate metal ion or by adding to the coordination sphere to yield a penta-coordinate metal ion with H2O as the fifth ligand (see Table V). In some cases an equilibrium between these two coordination geometries is also reported. 

Probably the most important effect contributed by metal coordination to ligands is stereochemical in nature. Because of the rather strict coordination geometry imposed by metal ions, ligands can be held in suitable juxtaposition for reactions to take place between them. This phenomenon is the hallmark of metal template reactions and is also a crucial feature of metal enzyme reactions, where high specificity occurs. 

The d-d, CD and MCD spectra of cobalt carbonic anhydrase are pH dependent, as noted earlier. In general the d-d and MCD spectra of the enzyme in acidic pH resemble those of Co11 complexes of tetrahedral geometry. The spectra at alkaline pH are different from the spectra at acid pH, and suggest the presence of a distorted five-coordinate cobalt(II) centre. Thus it appears that in the active form of the enzyme the metal is present in a five-coordinate geometry. 

If our postulates are correct the most interesting feature of P-450 is the manner in which the protein has adjusted the coordination geometry of the iron and then provided near-neighbour reactive groups to take advantage of the activation generated by the curious coordination. Vallee and Williams (68) have observed this situation in zinc, copper and iron enzymes and referred to it as an entatic state of the protein. It is also apparent that some such adjustment of the coordination of cobalt occurs in the vitamin B12 dependent enzymes. As a final example we have looked at the absorption spectra of chlorophyll for its spectrum is in many respects very like that of a metal-porphyrin. This last note is intended to stress the features of chlorophyll chemistry which parallel those of P-450. 

Some efforts have been made to interpret the spectroscopic and magnetic properties of cobalt enzymes in terms of coordination geometry and chemical identity of ligands. The basis of these attempts is a comparison with the corresponding properties of low-molecular weight complexes of known structure. A brief summary of relevant data on some models is given in the following section. 

Compared with the heme proteins discussed in Section 2.2, the non-heme iron proteins presented here have a much more flexible coordination geometry. Taken together with the differences in electronic properties - heme enzymes contain mostly low-spin iron whereas non-heme enzymes contain mostly a high-spin iron - this is responsible for the more diverse chemistry found for the non-heme iron proteins. The great versatility of these enzymes makes them a treasure trove for the development of iron-based catalysts. Inspired by their biological archetypes, numerous catalytic reactions await to be reproduced by iron catalysts in organic synthesis. 

Ni+ center in two forms of EPR-silent Ni2 + methyl coenzyme M reductase was characterized by EPR and 14N ENDOR of cryoreduced enzyme.77 Based on these cryoreduction experiments, the reduced form of this protein was definitely assigned to the Ni1 + valence state, ending previous ambiguities, and the coordination geometry of the metal center was determined for two forms of the enzyme. 

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