Catalytic Mechanism of Chorismate Mutase

Catalytic Mechanism of Chorismate Mutase 119 Table 1.4 Relationship between the free energies in different environments. ... 

The conversion of [49] into [50] involves a Claisen rearrangement. Once this was realized it was less surprising that no specific catalytic groups on the enzyme are involved. Support for the Claisen-type mechanism comes from the inhibition shown by the bicyclic dicarboxylate [51], prepared by Bartlett and Johnson (1985) as an analogue of the presumed transition state [52], This same structure [51], coupled through the hydroxyl group to a small protein, was used as a hapten to induce antibodies, one (out of eight) of which mimics the behaviour of chorismate mutase, albeit less efficiently (Table 7). 

Guo H, Q Cui, WN Lipscomb, M Karplus (2001) Substrate conformational transitions in the active site of chorismate mutase Their role in the catalytic mechanism. Proc. Natl. Acad. Sci. U. S. A. 98 (16) 9032-9037... 

The two independent studies of chorismate mutase were motivated by the fact that this enzyme does not exchange atoms or electrons with the substrate during the catalysis. Chorismate mutase catalyzes the rearrangement of chorismate to prephenate with an enhancement of the reaction rate of 2 x 10 compared to the reaction in solution. The catalytic mechanism was modeled using both semiempirical AMl/MM [70] and ab initio HF/MM and MP2/MM [71] hybrid potentials. The conclusions from both investigations were similar ... 

The partitioning of the system in a QM/MM calculation is simpler if it is possible to avoid separating covalently bonded atoms at the border between the QM and the MM regions. An example is the enzyme chorismate mutase [39] for which the QM region could include only the substrate, because the enzyme does not chemically catalyze this pericyclic reaction. In studies of enzyme mechanisms, however, this situation is exceptional, and usually it will be essential, or desirable, to include parts of the protein (for example catalytic residues) in the QM region of a QM/MM calculation, i.e. the boundary between the QM and MM regions will separate covalently bonded atoms (Fig. 6.1). 

COMT is, for many of the same reasons as with chorismate mutase, well suited for the study with computational techniques. The reaction mechanism it catalyzes is the same mechanism that operates in the absence of the enzyme, specifically, the S 2 mechanism, facilitating comparison of the bare solution-phase reaction with the catalyzed reaction. The subsfiate and cofactor do not covalendy bind to the enzyme, so that defining the QM region and the MM region should be relatively uncomplicated. Lasdy, the X-ray crystal structure of COMT bound with the inhibitor 3,5-dinitrocatechol has been determined with a resolution of 2 kP An interesting twist to this enzyme is that the active site includes a metal cation, Mg " ". This crystal structure allows for a natural starting point for computational exploration of the means of the catalytic action of COMT. The rate acceleration provided by COMT is substantial the reaction is 10 times faster within the enzyme than in solution. " ... 

Catalytic antibodies are capable of catalyzing reactions normally carried out by enzymes, albeit usually with much lower efficiency. Interestingly, an x-ray crystallographic analysis of the structure of a catalytic antibody that mimics chorismate mutase showed that it uses essentially the same mechanism to carry out the reaction (45), A similar finding was made for a catalytic antibody with a serine protease active site (46), Both of these observations are fascinating because while enzymes evolved over millions of years, the catalytic antibodies were generated in only a matter of weeks. 

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