Polyprotein processing is one of the major strategies employed by both animal and plant viruses to generate more than one functional protein from the same polypeptide chain. To accomplish cleavage at specific sites, viruses employ one or more proteases with unique cleavage specificities. Plant viruses of the Solemoviridae [E1] and subgroup II Luteoviridae [E2] families and the mycovirus of the Barnaviridae [E3] family contain an N-terminal serine protease domain of the S39 family that is responsible for the processing of the polyprotein both in cis and in trans [E4]. A triad composed of a histidine, an aspartate and a serine residue constitute the active centre of the peptidase S39 family domain [1,2,3,4].

The peptidase family S39 domain consists of two β barrrels (domains I and II) connected by a long inter-domain loop (see <PDB:1ZYO>). Both the domains belong to the all β class of proteins. There are only three helices in the peptidase S39 domain [4]. The active site and the substrate-binding cleft occur in between the two domains and are fairly exposed to the solvent. The active site histidine forms hydrogen bonds with both serine and aspartate, the other two residues of the catalytic triad [4].

The profile we developed covers the entire peptidase family S39 domain.