Family S31


Summary Holotypes Alignment Tree Genomes Structure Literature Architecture

Summary for family S31

Family type peptidaseS31.001 - pestivirus NS3 polyprotein peptidase (bovine viral diarrhea virus 1), MEROPS Accession MER0001634 (peptidase unit: 1590-1800)
Content of familyPeptidase family S31 contains a polyprotein processing endopeptidase from pestiviruses.
History Identifier created: Methods Enzymol. 244:19-61 (1994)
Pestiviruses are single-stranded RNA viruses closely related to flaviviruses and hepatitis C virus. The genus Pestivirus contains viruses causing bovine viral diarrhea, classical swine fever of pigs and border disease of sheep. The pestivirus genome encodes a single, 4000-residue polyprotein which is processed by host as well as virus-encoded endopeptidases. That the pestivirus polyprotein component NS3 (also known as p80) was an endopeptidase distantly related to trypsin was predicted by Gorbalenya et al., 1989 and Bazan & Fletterick, 1989, and activity was first shown by Wiskerchen & Collett, 1991. The Npro component is a second endopeptidase, in family C53.
Catalytic typeSerine
Active site residuesH1658 D1686 S1752 
Active siteThe active site triad consists of His1658, Asp1686 and Ser1752. These residues have been identified by site-directed mutagenesis (Wiskerchen & Collett, 1991, Tautz et al., 2000) (see the Alignment). Unusually for a member of clan PA, Asp1686 is followed by a glutamate rather than a hydrophobic residue and Ser1752 is preceded by a tryptophan rather than an aspartate (see the Alignment for clan PA, subclan S).
Activities and specificitiesThe NS3 endopeptidase cleaves each pestivirus polyprotein at four positions, between NS3 and NS4, NS4A and NS4B, NS4B and NS5A, and between NS5A and NS5B. These are all the cleavages that occur C-terminal to the NS3 protein. In all cleavages, the P1 residue is Leu, and in all except one, P1" is Ser, the exception being the NS4A/NS4B cleavage site in which it is Ala. The NS3/NS4A cleavage occurs in cis, but all the others in trans. NS4A is an essential co-factor for activity.
Molecular structureNo tertiary structure has been determined for the NS3 endopeptidase; the family is included in clan PA because the active site residues are in the same order in the sequence as in chymotrypsin (S01.001). To be functionally active, NS3 has to form a complex with NS4A, which is dependent on the six N-terminal residues of NS3; truncation of NS3 prevents the binding of NS4A and abbrogates proteolysis (Tautz et al., 2000). Uncleaved NS2-3 (also known as p125) also has proteolytic activity.
Basis of clan assignmentActive site residues for members of this family and family S1 occur in the same order in the sequence: H, D, S.
Distribution of family Bacteria -  
Archaea -  
Protozoa -  
Fungi -  
Plants -  
Animals -  
Viruses details  
Biological functionsThe NS3 endopeptidase is essential for viral replication (Xu et al., 1997). The N-terminus of NS2-3 is generated by host cell signalase (XS26-001). Release of NS3 from NS2-3 only occurs in cytopathogenic strains of pestivirus, but the peptidase responsible for the cleavage has not yet been identified (Kummerer et al., 1998).
Statistics for family S31Sequences:32
Identifiers with PDB entries:1
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Other databases INTERPRO IPR000280
PFAM PF05578
Peptidases and Homologues MEROPS ID Structure
pestivirus NS3 polyprotein peptidaseS31.001Yes
Family S31 unassigned peptidasesunassigned-