Ethanol could be deactivating your enzyme. Instead, try ammonium sulphate as a precipitating agent.

Do you have any idea wrt the concentration of the protein in the supernatants? Precipitation works well for fairly concentrated proteins; otherwise it is not worth the hassle. If you have access to a diafiltration system try that, or else, run the supernatant through an ion exchanger and test the resulting fractions.

Ethanol may denatured your protein, you can try ammonium sulphate or ice cold acetone precipitation... 

I tried using ice cold acetone to precipitate plant proteins, and it worked, though maintained only partial of my enzyme activity. Ethanol might not be a good choice to precipitate proteins.

You can drip your protein extract into ice cold acetone (cooled beforehand at -20 o/n) that is placed on ice, while stirring using a magnetic stirrer. You shall be able to observe precipitation straight away when the protein extract is dripped into the cold acetone. After centrifugation, harvest the protein pellets and dry it at RT until only a few drops of acetone remained in the tube (do not dry the pellets o/n or else you will get dry powders). That small fraction of acetone remained with your pellet will ease solubilization of your protein next time. Store the protein pellets at -20 until use, it should be stable for a few months (~ 6 mths).

Hope this helps.

Thank you all for your valuable suggestions. That helped me lot. 

I did ammonium sulphate precipitation and got brownish pellet which is really sticky  and hard to handle. I used Citrate Phosphate butter at pH 4 for  resuspension.

Any idea how to handle this sticky pellet? to recover all of this?

Try isoelectric focusing and zone electrophoresis. 

Thank you all for valuable suggestions.