I would suggest to treat your protein with a protease such as trypsin or chymotrypsin. This will cleave it into multiple smaller fragments and most probably leave your protein inactivated. Plenty of protocols can be found online.

You can check which fragments will be formed here: http://web.expasy.org/peptide_cutter/

Boiling with SDS should do it.

Hi..Mohamed..

Try to give some details of your protein so that we can provide much better suggestions....For example what kind of enzyme is your protein...Or what are critical residues for your protein for its activity if known...If your enzyme requires cysteine for its catalytic activity...You can try to add some Iodoacetamide...this will irreversible inactivate your protein...So on... As Adam Shapiro and Giel Detienne have suggested treating your recombinant protein with protease or SDS will do the job in general...