Both the substrates as well the enzymes do not undergo denaturation since the enzyme was incubated with the substrate and it lost its activity.
When a certain substrate comes into contact with an enzyme, it will bind to the active region. Binding of the substrate to the active region of the protein results in the formation of a more stable enzyme substrate complex. This is because the enzyme substrate complex is more resistant to heat denaturation than just the enzyme.
Because the enzyme-substrate complex ground state has a lower energy level, more energy is required to overcome this energy barrier and denature the enzyme. In the question, it is given that 3% of the enzyme lost its activity, which might have happened when the enzyme and the substrate were incubated. Only 3% of the enzyme was liberated after the denaturation step, leaving 97% occupied with substrate.
As a result, neither the enzyme nor the substrate undergoes denaturation.
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