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