I am currently writing a report on the effect of pH on the enzyme pectinase but I havn't been able to find a specific description of what happens to the enzyme at a molecular level if the pH of its environment is outside of the recommended optimum. I'm trying to understand what happens in more detail than just "it changes its shape". (i.e. how exactly do the active sites change and by what process does this occur)
The change in activity of an enzyme as a function of pH may simply be due to a change in the ionization of side chains that participate in the active site reaction mechanism. Those with ionizable side chains include Asp, Glu, His, Cys, Tyr, Lys, and Arg.
There are also usually many amino acids with ionizable side chains on the surface of the protein (add the amino and carboxy termini to the above list), and changing their ionization can alter the folding of the protein, leading to exposure of normally buried hydrophobic residues. If the protein's structure is sufficiently perturbed, it may unfold (denature) to the extent that the exposure of the hydrophobic core causes the protein to become insoluble in water or to aggregate with other molecules of the same protein, and precipitation will occur.
Might be this book help you.
Chapter 7: Structural and Biochemical Properties of Pectinases: Pg 99-117
Book: Industrial Enzymes, Structure, Function and Applications:
Published by Springer, Authors:Julio Polaina and Andrew P. MacCabe
Difference in pH from the optimum might not directly impact on the structural integrity of the enzyme. It might be that the active residues for catalysis are not available for reaction due to ionization of the R group. This is dependent on the catalytic mechanism the enzyme employs.
An enzyme is however denatured (changed in conformation) when the structural backbone is altered such that the enzyme cannot bind with the substrate or react with the binded substrate for catalysis to occur. Here, a partial or complete loss of activity is experienced.
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