The part of an enzyme that does the business. Since metabolites are generally on the order of amino acid size (10-29 atoms), wheras most enzymes are 100s of residues (therefore thousands of atoms) it is a little like a jigsaw with one piece missing. The reason for this disparity in sizes is partially necessity and partially chance. Or rather, the enzyme is large through necessity - which produces higher order interactions - which have to be maintained by evolution. There is an obvious advantage for enzymes to be as small as possible, but not at the cost of loss of allostery or regulation.

So why so large to start with? Well, the catalytic groups have to be positioned fairly precisely for a reaction to take place. To start with, they must be in the same region of space, which can only really be provided by a large framework. These reactive groups must also be shielded from solvent, to preserve pH and electrostatics and so on. An analagous situation is an electronics product - the components must be close together, and enclosed in an attractively coloured plastic shell.

Fine tuning is best achieved when acting on a flexible frame that can be modified stepwise to improve efficiency. Like sculpting, you start with a large block and cut away as well as adding bits on. The catalytic triad is a good example of convergent evolution of active sites, where the frameworks (eg subtilisin and chymotrypsin) are different, but the catalytic geometry is the same.

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