Peptidase is an umbrella term recommended by the International Union of Biochemistry and Molecular Biology and the Human Gene Nomenclature Committee. It is also commonly used in the MEROPS database. Peptidase is used to describe any enzyme that is capable of catalyzing the hydrolysis of a protein substrate and breaking it down into smaller polypeptides or amino acids. These proteins are also often referred to as protease or proteinase.
Peptidases are a key component of a number of common biological functions. The most obvious is in the digestion of eaten proteins. Without peptidase, the catalyzation might take years or even centuries. They also assist in the breakdown of old proteins (catabolism) as well as cell signaling. They occur in mammals, plants, bacteria and even viruses.
Peptidase Mechanism and Function
Peptidase breaks protein compounds down into amino acids by leaving the peptide bonds within proteins by hydrolysis. This means that water is used to break the bonds of protein structures.
This is achieved through one of the following two mechanisms depending on the specific kind of peptidase. Aspartic, glutamic and metallo peptidases, activate a water molecule. This in turn performs a nucleophilic (electron donating) attack on the peptide bond to hydrolyze it.
Serine, threonine and cysteine peptidases, form a nucleophilic residue which occurs as part of a catalytic triad. This residue performs the same nucleophilic attack albeit to different effect. The attack covalently bonds the peptidase to the substrate protein and the first half of the product is released. This covalent acyl-enzyme intermediate is subsequently hydrolyzed by activated water. This completes the catalysis by releasing the second half of the product and the free enzyme is regenerated.
Peptidases are classified based on their interactions and the nature of their catalysis. Each group of peptidases uses a different catalyst to facilitate one of the above mechanisms.
Some of these enzymes can be highly promiscuous, hydrolyzing a wide range of protein substrates. Others, however, can be very specific and cleave substrates in certain sequences to achieve precise events. The serine peptidase Thrombin, for example, requires this kind of specificity to facilitate blood clotting.
It’s worth noting that, as proteins, peptidases can also be cleaved by other peptidases, sometimes of the same variety.