Zinc peptidases are the best known of the zinc enzymes and are described in more detail than other zinc enzymes at the beginning of this chapter, followed by some examples of the catalytic mechanisms of other mono- and multi-zinc enzymes. This article describes the mechanism of action and the role of zinc ions in catalysis for only a few prototypical zinc enzymes (being a reference standard for others).
3.1. Zinc proteases.
Among the monozinc proteases, thermolysin and carboxypeptidase A are believed to be the prototypical model for studying the mechanism of action. The remaining enzymes in this group have a similar presumed catalytic mechanism and may differ in some details (zinc ligands, the enzyme residues that interact with the substrate). Therefore, the mechanism of action of these model enzymes in this class is described in some detail and then the comparison of monozinc peptidases is presented.
Crystallographic analyzes of enzyme-inhibitor complexes are used to suggest how enzymes interact with their substrates. Properly chosen inhibitors can provide structural models for various stages of catalysis, including the Michaelis complex, transition states, and products. These studies may suggest a possible catalysis mechanism. The details of the putative catalytic pathways can be explored in detail through model building and computer graphics. However, very useful long-lasting inhibitor-enzyme complexes may provide only structural models for different stages of catalysis, but are obviously not true intermediates and, in the absence of supporting data, should be interpreted with caution.
Bacillus thermoproteolyticus thermolysin is a thermostable zinc endopeptidase, containing zinc ion (essential for catalysis) and four calcium ions, necessary for its thermal stability. In native thermolysin, the zinc ion has approximate tetrahedral coordination with three ligands provided by the protein (His 142, His 146 and Glu 166) and the fourth provided by a water molecule (Figure 5).