Enzymes catalyze the biochemical reactions in cells of all organisms. These reactions constitute the chemical basis of life. Most enzymes are proteins—a few are ribonucleic acids or ribonucleoproteins—and the catalytic machinery is located in a relatively small active site, where substrates bind and are chemically processed into products. Illustrations of the molecular structure of chymotrypsin, a typical enzyme, and the location of its active site appear in figs. 1-1A and B. The polypeptide chain is shown as a ribbon diagram, and the active site is the region in which an inhibitor, the black ball-and-stick model, is bound. The gray ball-and-stick structures are amino acid side chains at the active site that participate in catalysis. The ribbon diagram shows the individual chains and the α-helices and β-strands as if there were vacant spaces between them; however, very little free space exists in the interior of an enzyme. The packing density in the interior of a protein is typically 0.7 to 0.8, meaning that 70% to 80% of the space is filled and only 20% to 30% is interstitial space (Richards, 1974). That the packing density in hexagonally closest packed spheres is 0.75, similar to a protein, conveys a concept of the interior. The free space inside a protein is so little that in a space-filling model, the polypeptide chain cannot be discerned, and interactions between active sites and substrate or inhibitors cannot be seen. For this reason, we display structures as ribbon diagrams to facilitate the discussion of ligand binding interactions within an active site. Chymotrypsin is the most widely studied and one of the best-understood enzymes. It catalyzes the hydrolysis of proteins at the carboxamide groups of hydrophobic amino acid residues, principally phenylalanyl, tyrosyl, and tryptophanyl residues. It also catalyzes the hydrolysis of small substrates, such as acetyltyrosine ethyl ester (ATEE) or acetyltyrosine p-nitroanilide (ATNA). These reactions are practically irreversible, their rates can be measured spectrophotometrically, and they behave kinetically as one-substrate enzymatic reactions. The overall reaction of ATEE can be written as ATEE → Acetyltyrosine + Ethanol, where the participation of water as a substrate is understood.
Sequence around the Active Center Cystine of Lipoamide Dehydrogenase from Pig Heart, Comparison with the E. coli Enzyme
