In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- Each clan is identified with two letters the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine threonine and cysteine). Some families cannot yet be assigned to clans and when a formal assignment is required such a family is described as belonging to clan A- C- M- N- S- T- or U- according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan for example MA(E) the gluzincins and MA(M) the metzincins.
- Peptidase families are grouped by their catalytic type the first character representing the catalytic type: A aspartic; C cysteine; G glutamic acid; M metallo; N asparagine; S serine; T threonine; and U unknown. The serine threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic glutamic and metallopeptidases the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases the nucleophile is asparagine and all are self-processing endopeptidases.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies which can be seen not only in their three-dimensional structures but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related) and further sub-divided into families on the basis of the architecture of their catalytic dyad or triad
. This group of proteins belong to the peptidase family C1 sub-family C1A (papain family clan CA). It includes proteins classed as non-peptidase homologues. These are have either been shown experimentally to lack peptidase activity or lack one or more of the active site residues. The papain family has a wide variety of activities including broad-range (papain) and narrow-range endo-peptidases aminopeptidases dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity
. Members of the papain family are widespread found in baculovirus
eubacteria yeast and practically all protozoa plants and mammals
. The proteins are typicallylysosomal or secreted and proteolytic cleavage of the propeptide is required for enzyme activation although bleomycin hydrolase is cytosolic in fungi and mammals
. Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions. The propeptide regions serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate
.The catalytic residues of papain are Cys-25 and His-159 other important residues being Gln-19 which helps form the 'oxyanion hole' and Asn-175 which orientates the imidazole ring of His-159.