Chorismate mechanism

In this contribution, we describe work from our group in the development and application of alternatives that allow the explicit inclusion of environment effects while treating the most relevant part of the system with full quantum mechanics. The first methodology, dubbed MD/QM, was used for the study of the electronic spectrum of prephenate dianion in solution [18] and later coupled to the Effective Fragment Potential (EFP) [19] to the study of the Claisen rearrangement reaction from chorismate to prephenate catalyzed by the chorismate mutase (CM) enzyme [20]. 

Chorismate mutase catalyzes the Claisen rearrangement of chorismate to prephenate at a rate 106 times greater than that in solution (Fig. 5.5). This enzyme reaction has attracted the attention of computational (bio)chemists, because it is a rare example of an enzyme-catalyzed pericyclic reaction. Several research groups have studied the mechanism of this enzyme by use of QM/MM methods [76-78], It has also been studied with the effective fragment potential (EFP) method [79, 80]. In this method the chemically active part of an enzyme is treated by use of the ab initio QM method and the rest of the system (protein environment) by effective fragment potentials. These potentials account... 

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). 

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). 

Figure 1. Hypothetical mechanism for shuttling of intermediates of the common aromatic pathway between plastidic and cytosolic compartments. Enzymes denoted with an asterisk (DAHP synthase-Co, chorismate mutase-2, and cytosolic anthranilate synthase) have been demonstrated to be isozymes located in the cytosol. DAHP molecules from the cytosol are shown to be shuttled into the plastid compartment in exchange for EPSP molecules synthesized within the plastid. Abbreviations C3, phosphoenolpyruvate C4, erythrose 4-P DAHP, 3-deoxy-D-arabino-heptulosonate 7-phosphate EPSP, 5-enolpyruvylshikimate 3-phosphate CHA, chorismate ANT, anthranilate TRP, L-tryptophan PPA, prephenate AGN, L-arogenate TYR, L-tyrosine and PHE, L-phenylalanine.

We have examined the time course of changes induced in isozymes of chorismate mutase and DAHP synthase in potato tubers following mechanical wounding (Table III). In each case both isozymes responded—the plastidic isozyme responding sooner and to a greater extent than the cytosolic isozyme. All five of the other pathway enzymes so far examined were induced by mechanical wounding. 

Elimination of P from 5-enolpyruvylshikimate 3-P (Eq. 25-3 and Fig. 25-1, step g) produces chorismate.30 The 24-kDa chorismate synthase, which catalyzes this reaction, requires for activity a reduced flavin. Although there is no obvious need for an oxidation reduction coenzyme, there is strong evidence that the flavin may play an essential role in catalysis, perhaps via a radical mechanism.31-331 ... 

Chemical properties appropriate to a compound found at a branch point of metabolism are displayed by chorismic acid. Simply warming the compound in acidic aqueous solution yields a mixture of prephen-ate and para-hydroxybenzoate (corresponding to reactions h and l of Fig. 25-1). Note that the latter reaction is a simple elimination of the enolate anion of pyruvate. As indicated in Fig. 25-1, these reactions correspond to only two of several metabolic reactions of the chorismate ion. In E. coli the formation of phe-nylpyruvate (steps h and i, Fig. 25-1) is catalyzed by a single protein molecule with two distinctly different enzymatic activities chorismate mutase and prephenate dehydratase.34-36 However, in some organisms the enzymes are separate.37 Both of the reactions catalyzed by these enzymes also occur spontaneously upon warming chorismic acid in acidic solution. The chorismate mutase reaction, which is unique in its mechanism,373 is discussed in Box 9-E. Stereochemical studies indicate that the formation of phenylpyruvate in Fig. 25-1, step z, occurs via a... 

Fig. 6 Four enzymes (one salicylate-AMP ligase YbtE/PchD, two NRPS and/or NRPS/PKS enzymes HMWPl/PchE and HMWP2/PchF, and one reductase YbtU/PchG) are required for the in vitro biosynthesis of (a) yersiniabactin (24) and (b) pyochelin (25). (c) The initial stages of 24 and 25 biosynthesis proceed via a similar mechanism from chorismic acid 26 to the salicylate-bisthiazole intermediate 33...

Fig. 12 The initial stages of 64, 65, and 66 biosynthesis proceed via the same mechanism, with the condensation of DHB (75) (from chorismic acid 26) with a PCP-tethered amino acid 80 (serine (a), lysine (b), or threonine (c), respectively)...

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... 

Chorismate mutase catalyses the Claisen rearrangement of chorismate to form prephenate. It is an excellent system for analysing catalysis because the same reaction occurs in solution with the same reaction mechanism no covalent catalysis by the... 

Woodcock HL, M Hodoscek, P Sherwood, YS Lee, HF Schaefer, BR Brooks (2003) Exploring the quantum mechanical/molecular mechanical replica path method a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase. Theor. Chem. Acc. 109 (3) 140-148... 

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... 

Lee YS, SE Worthington, M Krauss, BR Brooks (2002) Reaction mechanism of chorismate mutase studied by the combined potentials of quantum mechanics and molecular mechanics. J. Phys. Chem. B 106 (46) 12059-12065... 

The results of these selection experiments are mechanistically significant insofar as they support a critical role for a cation in the mechanism of chorismate mutase. No active catalysts were found that lacked a cation in the vicinity of the substrate s ether oxygen. The conclusion that a cation is crucial for high chorismate mutase activity can thus be made with much greater confidence than would have been possible following a conventional mutagenesis experiment in which only single substitutions were considered [66]. Of course, we cannot exclude the possibility that other, equally effective... 

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. " ... 

Quantum mechanical calculations can be used to obtain estimates of molar entropies of species. An example is the study of the conversion of chorismate to prephenate by Kast and coworkers (11). They used quantum mechanics to estimate Ar5° for chorismate (aq) = prephenate (aq). Since Af//° was obtained experimentally, this made it possible to estimate the equilibrium constant for this reaction. 

A novel mechanism for regulating transcription in bacteria was discovered by Charles Yanofsky and his colleagues as a result of their studies of the tryptophan operon. The 7-kb mRNA transcript from this operon encodes five enzymes that convert chorismate into tryptophan (Section 24.2.10). The mode of regulation of this operon is called attenuation, and it... 

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