The genome of pestiviruses [E1] is a single plus-strand RNA and contains a
single large open reading frame (ORF), a 5' untranslated region (5'UTR) and a
3' untranslated region (3'UTR). The ORF encodes a polyprotein, which is
processed by viral and cellular proteases into mature proteins (the structural
proteins in the N-terminal portion of the polyprotein whilst the replicative
(non-structural or NS) proteins constitute the remainder). The pestivirus NS3
protein is a multifunctional protein possessing serine protease, RNA helicase
(see <PDOC51192>), and a nucleoside triphosphatase (NTPase) activities
located in two functionally distinct domains. The N-terminal one-third of
pestiviral NS3 primarily serves as a protease to process the viral
polyprotein. The helicase and NTPase activities are localized to the C-terminal of NS3 protein. The NS3 protease (NS3pro) domain is of some 180 aa
with a catalytic triad of His-Asp-Ser. Positive regulation (activation) is
observed by its interaction with NS4A. The pestivirus NS3pro domain forms
peptidase family S31 of clan PA [E2].
The profile we developed covers the entire pestivirus NS3pro domain.
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