Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor"

To obtain a clearer understanding of the forces involved in transition state stabilization by Escherichia coli cytidine deaminase, we investigated the thermodynamic changes that accompany substrate binding in the ground state and transition state for substrate hydrolysis. Viscosity studies indicate that the action of cytidine deaminase is not diffusion-limited. Thus, K-m appears to be a true dissociation constant, and k(cat) describes the chemical reaction of the ES complex, not product release. Enzyme-substrate association is accompanied by a loss of entropy and a somewhat greater release of enthalpy. As the ES complex proceeds to the transition state (ESdouble dagger), there is little further change in entropy, but heat is taken up that almost matches the heat that was released with ES formation. As a result, k(cat)/K-m (describing the overall conversion of the free substrate to ESdouble dagger) is almost invariant with changing temperature. The free energy barrier for the enzyme-catalyzed reaction (k(cat)/K-m) is much lower than that for the spontaneous reaction (k(non)) (Delta Delta G(double dagger) = -21.8 kcal/mol at 25 degrees C). This difference, which also describes the virtual binding affinity of the enzyme for the activated substrate in the transition state (S'), is almost entirely enthalpic in origin (Delta Delta H = -20.2 kcal/mol), compatible with the formation of hydrogen bonds that stabilize the ES' complex. Thus, the transition state affinity of cytidine deaminase increases rapidly with decreasing temperature. When a hydrogen bond between Glu-91 and the 3'-hydroxyl moiety of cytidine is disrupted by truncation of either group, k(cat)/K-m and transition state affinity are each reduced by a factor of 10(4). This effect of mutation is entirely enthalpic in origin (Delta Delta H similar to 7.9 kcal/mol), somewhat offset by a favorable change in the entropy of transition state binding. This increase in entropy is attributed to a loss of constraints on the relative motions of the activated substrate within the ESdouble dagger complex. In an Appendix, some objections to the conventional scheme for transition state binding are discussed.