Question

5. A protonated histidine residue in the active site of aspartate transcarbamoylase, ATCase, is thought to be important in stabilizing the transition state of the bound substrate. a) Sketch a graph showing the pH dependence of the catalytic rate, assuming that this interaction is essential and dominates the pH-activity profile of the enzyme. Provide the biochemical basis for your graph. b) Identify one of the two substrates involved in the reaction catalyzed by ATCase and the enzyme class for ATCase. c) The ATCase mechanism is known to proceed via an ordered mechanism. Draw a Cleland notation diagram showing how this reaction proceeds. Abbreviate the second substrate as CP. Two products are formed.

Answer 1

Transcarbamoylase (ATCase) is an allosterically regulated enzyme with unique quaternary structure involving separable catalytic and regulatory subunits. This allosteric regulation affects the kinetics of the enzyme. Structure ATCase consists of two catalytic trimers and three regulatory dimers that are completely separable units. It has been documented that the subunits can even combine when mixed together, reconstituting the enzyme. The two catalytic trimers are arranged on top of each other, with three dimers of the regulatory chains combining them. This scene is only looking at one set of regulatory and catalytic subunits, not all of them for the sake of visualization. Significant interactions between the regulatory dimers and catalytic trimers occur; such as catalytic trimer chains contacting structural domains in the regulatory unit that are stabilized by a zinc atom bound to four cysteine residues. ATCase is largely alpha helical with large changes in quaternary structure occurring (trimers move 12 Angstroms apart and rotate approximately 10 degrees) upon PALA binding (a bisubstrate analog that resembles an intermediate). The PALA interactions are as shown. Function Aspartate Transcarbamoylase catalyzes the first step in the biosynthesis of pyrimidines ( specifically called N-carbamoyl-aspartate) which ultimately yield pyrimidine nucleotides such as CTP (Cytidine Triphosphate). The cell must precisely regulate the amount of CTP in the cell because making it can be energetically expensive. Therefore, the rate of reaction catalyzed by ATCase is fast at low [CTP] but slows as [CTP] increases. However, CTP is quite different than the active site of ATCase, so at high levels it effectively inhibits the enzyme by binding to an allosteric/regulatory site rather than the active site. This inhibition by CTP is an example of feedback inhibition. ATCase is a textbook example of a molecule under allosteric regulation in which the binding of substrate to one active site in a molecule increases the likelihood that the enzyme will bind more substrate, a phenomena called cooperativity. Mechanism ATCase displays features of a concerted mechanism due to the fact that changes in the enzyme are "all or none". In Michaelis-Menten kinetics, ATCase's curve is sigmoidal exemplifying a union of the R (active) and T (tense) states. It is essential to grasp that the enzyme is in equilibrium between the T and R states; High concentrations of CTP shift the curve right towards the T state, whereas high concentrations of ATP shift the curve left towards the R state. Allosterically regulated enzymes such as ATCase do not follow Michaelis-Menten kinetics. Allosteric enzymes differ from traditional enzymes in that they are affected by not only substrate concentration but also regulation by other molecules, as demonstrated by CTP in the above example. Example of substrate are 1.ATCase catalyse the condensation of aspartate and carbamoyl phosphate to form N-carbomylasprtate,in pyrimidine synthesis 2. Modification of cysteine residues p-Hydroxymercuribenzonate react with crucial cysteine in APCase