Arteriviruses are enveloped, positive-stranded RNA viruses and include pathogens of major economic concern to the swine- and horse-breeding industries [E1]:

  - Equine arteritis virus (EAV).
  - Porcine reproductive and respiratory syndrome virus (PRRSV).
  - Mice actate dehydrogenase-elevating virus.
  - Simian hemorrhagic fever virus.

The arterivirus replicase gene is composed of two open reading frames (ORFs). ORF1a is translated directly from the genomic RNA, whereas ORF1b can be expressed only by ribosomal frameshifting, yelding a 1ab fusion protein. Both replicase gene products are multidomain precursor proteins which are proteolytically processed into functional nonstructural proteins (nsps) by a complex proteolytic cascade that is directed by four (PRRSV/LDV) or three (EAV) proteinase domains encoded in ORF1a. The arterivirus replicase processing scheme involves the rapid autoproteolytic release of two or three N-terminal nsps (nsp1 (or nsp1α/1β) and nsp2 (see <PDOC51538>)) and the subsequent processing of the remaining polyproteins by the "main protease" residing in nsp4 (see <PDOC51493>), together resulting in a set of 13 or 14 individual nsps. The arterivirus nsp1 region contains a tandem of papain-like cysteine autoprotease domains (PCPα and PCPβ), but in EAV PCPα has lost its enzymatic activity, resulting in the 'merge' of nsp1α and nsp1β into a single nsp1 subunit. Thus, instead of three self-cleaving N-terminal subunits, EAV has two: nsp1 and nsp2. The PCPα and PCPβ domains mediate the nsp1α|1β and nsp1β|2 cleavages, respectively. The catalytic dyad of PCPα and PCPβ domains is composed of Cys and His residues. In EAV, a Lys residue is found in place of the catalytic Cys residue, which explains the proteolytic deficiency of the EAV PCPα domain [1,2,3,4]. The PCPα and PCPβ domains form respectively peptidase families C31 [E2] and C32 [E3].

The PCPα and PCPβ domains have a typical papain fold, which consists of a compact global region containing sequentially connected left (L) and right (R) parts in a so-called standard orientation. The L subdomain of PCPα consists of four α-helices, while the R subdomain is formed by three antiparallel β strands (see <PDB:3IFU>) [5]. The L subdomain of the PCBβ consists of three α-helices, while the R subdomain is formed by four antiparallel β-strands (see <PDB:3MTV>) [6]. The Cys and His residues face each other at the L-R interface and form the catalytic center of the PCPα and PCPβ domains [5,6].

The profiles we developed cover the entire PCPα and PCPβ domains.