Spumaviruses or foamy viruses (FVs) are a group of complex retroviruses that have been isolated from a number of animal species and are believed to be apathogenic in their animal host [E1]. FVs express a pol-specific transcript that codes for a Pol polyprotein that consists of the protease (PR), reverse transcriptase, robonuclease H , and the integrase domains. Retrovriral PRs belong to the family of aspartic proteases and are active as homodimers, with the active site triplets (Asp-Thr/Ser-Gly; D-T/S-G) from both chain contributing to the symetric active site of the enzyme. Transient FV PR domain homodimers are formed under native condition but are only present as a minor transient species, which is not detectable by traditional methods. Dimerization of FV RT might be triggered by additional viral or cellular factors [1,2,3,4]. The FV PR domain forms peptidase family A9 (spumapepsin family) [E2].

The FV PR domain consists of seven β-strands and a helical turn (see <pdb:2JYS>). The β-strands form a closed barrel-like β-sheet with the strand order β1-β2-β7-β3-β6-β5-β1. The strands β1 and β7 are arranged in parallel, while all other strands are arranged in an anti-parallel manner [3].

The profile we developed covers the entire FV PR domain.