Question

VI You are studying the mechanism of catalysis for an enzyme and find that mutating an active site lysine to glutamate has no effect on initial binding, but it significantly decreases the rate at which the enzyme catalyzes its reaction. Predict how this mutation (Lys Glu) is affecting catalytic rate in three sentences or fewer. (Hint, what might the lysine be doing to facilitate catalysis?) LMS stabilizes transition State

please help thanks

Answer 1

As we all know that, in an enzyme-catalyzed reaction, there are four steps involved. which are as follows:

Enzyme + Substrate -> enzyme-substrate complex -> Enzyme-product complex -> Enzyme + Product.

Here in the question, you have a mutated enzyme where the active site Lysine has been changed to Glutamic acid.

But this mutation does not affect initial binding, which means that the Lysine residue is playing some role in the intermediate steps.

Now if you consider the charge between two amino acids (Lys & Glu), then you will see that it has been changed from positive (Lysine) to negative (Glu).

So, after the mutation, the catalytic rate of the enzyme got significantly reduced. Now the predictions could be as follows:

1. The Lysine residue was somehow lowering the transition state energy by creating an environment to stabilize the transition state (intermediate states) by distributing its charge.

2. The positively charged amino acid was reacting with the substrate via covalent/salt bridge formation and was forming a lower energy intermediate transition state to bypass the main reaction pathway.

3. The polar residue (Lys) was distorting the bound substrates or rearranging it to reduce the reaction entropy, which was helping the enzyme to crossover the transition state.