Chorismate conformation

The differences in the rate constant for the water reaction and the catalyzed reactions reside in the mole fraction of substrate present as near attack conformers (NACs).171 These results and knowledge of the importance of transition-state stabilization in other cases support a proposal that enzymes utilize both NAC and transition-state stabilization in the mix required for the most efficient catalysis. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively.172 The fact that the reaction occurred faster in water than in methanol was attributed to greater stabilization of the TS in water by specific interactions with first-shell solvent molecules. The Claisen rearrangements of chorismate in water and at the active site of E. coli chorismate mutase have been compared.173 It follows that the efficiency of formation of NAC (7.8 kcal/mol) at the active site provides approximately 90% of the kinetic advantage of the enzymatic reaction as compared with the water reaction. 

Table 1.3 Energies and structural parameters for some chorismate conformers . ...

Schultz and coworkers (Jackson et a ., 1988) have generated an antibody which exhibits behaviour similar to the enzyme chorismate mutase. The enzyme catalyses the conversion of chorismate [49] to prephenate [50] as part of the shikimate pathway for the biosynthesis of aromatic amino acids in plants and micro-organisms (Haslam, 1974 Dixon and Webb, 1979). It is unusual for an enzyme in that it does not seem to employ acid-base chemistry, nucleophilic or electrophilic catalysis, metal ions, or redox chemistry. Rather, it binds the substrate and forces it into the appropriate conformation for reaction and stabilizes the transition state, without using distinct catalytic groups. 

The antibodies can also act like entropy traps by stabilizing a particular conformation of a substrate that is favorable to the formation of the TS. It is the case of the antibody 1F7 catalyzing the transformation of chorismate into prephenate," which stabilizes, thanks to several hydrogen bonds and an ionic bond between an arginine (Arg H95) and a carboxylate substituent of the substrate, the conformation of the chorismate which will give rise to the TS in a chair conformation for this reaction (Figure 11). 

Figure 11 Chorismate-prephenate rearrangement catalyzed by antibody 1F7 raised against a bicyciic hapten that mimics the chair conformation of the transition state of the reaction and X-ray structure of the corresponding antibody 1 F7-hapten compiex.

The reaction, which proceeds via a conformationally tight chair-type transition state, is clearly entropically dominated, with a AS of -13 eu. Whereas the known enzyme chorismate mutase from E. coli achieves a 3 x 106-fold accelerated catalysis, the antibody reaches a 104-fold enhancement. A decrease of AS to almost 0 eu points to the presence of an entropy trap. 

Figure 4.11). This reaction, a Claisen rearrangement, transfers the PEP-derived side-chain so that it becomes directly bonded to the carbocycle, and so builds up the basic carbon skeleton of phenylalanine and tyrosine. The reaction is catalysed in nature by the enzyme chorismate mutase, and, although it can also occur thermally, the rate increases some 106-fold in the presence of the enzyme. The enzyme achieves this by binding the pseudoaxial conformer of chorismic acid, allowing a transition state with chairlike geometry to develop. 

QM/MM methods have proved their value for enzyme reactions in differentiating between alternative proposed mechanisms, and in analysing contributions to catalysis. A current example is the analysis of the contribution of conformational effects and transition state stabilization in the reaction catalysed by the enzyme chorismate mutase.98,99 QM/MM calculations can be performed with... 

Ranaghan KE, AJ Mulholland (2004) Conformational effects in enzyme catalysis QM/MM free energy calculation of the NAC contribution in chorismate mutase. Chem. Comm. (10) 1238-1239... 

Marti S, J Andres, V Moliner, E Silla, I Tunon, J Bertran (2000) A QM/MM study of the conformational equilibria in die chorismate mutase active site. The role of the enzymatic deformation energy contribution. J. Phys. Chem. B 104 (47) 11308—11315... 

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... 

Guimaraes CRW, MP Repasky, J Chandrasekhar, J Tirado-Rives, WL Jorgensen (2003) Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase. J. Am. Chem. Soc. 125 (23) 6892-6899... 

Hur S, TC Bruice (2003a) Comparison of formation of reactive conformers (NACs) for the Claisen rearrangement of chorismate to prephenate in water and in the E-coli mutase The efficiency of the enzyme catalysis. J. Am. Chem. Soc. 125 (19) 5964-5972... 

The most favourable conformation for chorismic acid has the substituents pseudo equatorial but the L3,3]-sigmatropic rearrangement cannot take place in that conformation. First, the diaxial conformation must be formed and the chair transition state achieved. Then the required orbitals will be correctly aligned. 

The transition state for the enzymatic reaction has been shown to have a chairlike geometry as well [61], and conformationally constrained compounds that mimic this structure, such as the oxabicyclic dicarboxylic acid 1 (Fig. 3.6), are good inhibitors of chorismate mutase enzymes [62 - 64], How a protein might stabilize this high-energy species has been a matter of some debate. Recently, heavy atom isotope effects were used to characterize the structure of the transition state bound to BsCM [65]. A very... 

Fig. 3.6. Chorismate prefers a pseudodiequatorial conformation in solution. It must adopt a disfavored pseudodiaxial conformation to reach the pericyclic transition state. The conformationally constrained oxabicyclic dicarboxylic acid 1, which mimics the transition state, is a potent inhibitor of natural chorismate mutases [62], Antibodies raised against this compound also catalyze the reaction, albeit 100 to 10,000-times less efficiently than their natural counterparts [39, 41].

Bruice" countered that the very loose definition of the NAC meant that a far too large number of conformations of chorismate in water satisfied the criteria. With his more restrictive definition and using the AMI method, a similar population was found as in his original B3LYP study. 

Hur, S. Bruice, T. C. lust a near attack conformer for catalysis (chorismate to prephenate rearrangements in water, antibody, enzymes, and their mutants), J. Am. Chem. Soc. 2003,125, 10540-10542. 

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