Family S39

Family

Summary Holotypes Alignment Tree Genomes Structure Literature

S39A

Summary Holotypes Alignment Tree Genomes Literature

S39B

Summary Holotypes Alignment Tree Genomes Literature

Summary for family S39

Family type peptidaseS39.001 - sobemovirus peptidase (cocksfoot mottle virus), MEROPS Accession MER0001815 (peptidase unit: 131-319)
Content of familyFamily S39 contains polyprotein processing endopeptidases from RNA viruses.
History Identifier created: Handbook of Proteolytic Enzyme, Academic Press, London (1998)
The existence of a polyprotein processing endopeptidase in viruses related to southern bean mosaic virus (sobemoviruses) was first predicted by Gorbalenya et al., 1988. In the sobemoviruses and related luteoviruses, the genome encodes several proteins and polyproteins, and the number of genes is further enhanced by ribosomal frameshifting. The serine endopeptidase of family S63 is contained within the same polyprotein as the genome-linked VPg protein.
Catalytic typeSerine
Active siteActive site residues have been determined by site-directed mutagenesis for the endopeptidases from potato leaf roll luteovirus (S39.002; Sadowy et al., 2001) and Sesbania mosaic virus (S39.001; Satheshkumar et al., 2004) (see the Alignment).
Activities and specificitiesIn the potato leaf roll virus P1 polyprotein, processing occurs in trans (Li et al., 2000); whereas in the Sesbania mosaic virus the endopeptidase has been shown to cleave in (cis as well as trans (Satheshkumar et al., 2004). The endopeptidase from cocksfoot mottle virus cleaves two GluAsn bonds (Makinen et al., 2000) and that from the Sesbania mosaic virus cleaves two GluThr bonds and, suboptimally, a GluSer bond (Satheshkumar et al., 2004).
Molecular structureThe crystal structure of the peptidase from Sesbania mosaic virus (Gayathri et al., 2005) shows a chymotrypsin-like structure justifying the placing of family S39 in clan PA.
ClanPA
SubclanPA(S)
Basis of clan assignmentPredicted active 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 functionsCleavage of the viral polyprotein occurs between the protease and the VPg protein, and between the VPg protein and the RNA-dependent RNA polymerase, releasing these proteins from the polyprotein (Satheshkumar et al., 2004).
Statistics for family S39Sequences:66
Identifiers:2
Identifiers with PDB entries:1
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Subfamily S39A
Name Peptidase subfamily S39A
Subfamily type peptidase S39.001 - sobemovirus peptidase (cocksfoot mottle virus), MEROPS Accession MER0001815 (peptidase unit: 131-319)
Active site residues H176 D209 S276 
Statistics Sequences: 21
Identifiers: 1
Identifiers with PDB entries: 1
Other databases PFAM PF02122
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
sobemovirus peptidaseS39.001Yes
subfamily S39A non-peptidase homologuesnon-peptidase homologue-
subfamily S39A unassigned peptidasesunassigned-
Subfamily S39B
Name Peptidase subfamily S39B
Subfamily type peptidase S39.002 - luteovirus peptidase (potato leaf roll luteovirus), MEROPS Accession MER0011948 (peptidase unit: 204-399)
Active site residues H255 D286 S354 
Statistics Sequences: 45
Identifiers: 1
Identifiers with PDB entries: 0
Other databases INTERPRO IPR000382
PFAM PF02122
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
luteovirus peptidaseS39.002-
subfamily S39B unassigned peptidasesunassigned-