Hi Pankaj, there are tons of PDB protein structures available online.
Unfortunately, you will have to do some literature searchers to understand the enzyme catalytic mechanism.
Heaven forbid that you might even have to do some wet work in a real lab.
Doing experiments with real proteins is frustrating because somehow they don't behave like they should do on the computer.
If you do not know which amino acid residues in your enzyme participate in substrate binding and/or catalysis, you need to read the literature about your enzyme and find out. Once you have that information, you can go ahead and change the residues in the enzyme. Do it one mutation at a time. You might have to do some structure refinement before you can use that mutant - to make sure that the new amino acid you introduced fits snugly in its location. Then you can do two mutations that are compensating, to see if you can rescue the first mutation by the second, compensating, mutation. There are a lot of things you can do.
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