Family S39

Family

Summary Holotypes Alignment Tree Genomes Structure Literature Architecture

S39A

Summary Holotypes Alignment Tree Genomes Literature

S39B

Summary Holotypes Alignment Tree Genomes Literature

Summary for family S39

Family type peptidase	S39.001 - sobemovirus peptidase (cocksfoot mottle virus), MEROPS Accession MER0001815 (peptidase unit: 131-319)
Content of family	Family 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 type	Serine
Active site	Active 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 specificities	In 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 structure	The 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.
Clan	PA
Subclan	PA(S)
Basis of clan assignment	Predicted 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 functions	Cleavage 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 S39	Sequences:	71
	Identifiers:	2
	Identifiers with PDB entries:	2
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:	26
	Identifiers:	1
	Identifiers with PDB entries:	2
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
sobemovirus peptidase	S39.001	Yes
Subfamily S39A non-peptidase homologues	non-peptidase homologue	-
Subfamily S39A unassigned peptidases	unassigned	Yes

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 peptidase	S39.002	-
Subfamily S39B unassigned peptidases	unassigned	-