{PDOC51868}
{PS51868; PEPTIDASE_S39}
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* Peptidase family S39 domain profile *
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Polyprotein processing  is one of the major strategies employed by both animal
and plant  viruses  to generate more than one functional protein from the same
polypeptide chain.  To  accomplish  cleavage at specific sites, viruses employ
one or more proteases with unique cleavage specificities. Plant viruses of the
Solemoviridae [E1]   and  subgroup  II  Luteoviridae  [E2]  families  and  the
mycovirus of  the  Barnaviridae  [E3]  family  contain  an  N-terminal  serine
protease domain  of  the  S39 family that is responsible for the processing of
the polyprotein  both  in  cis  and  in  trans  [E4].  A  triad  composed of a
histidine, an  aspartate  and a serine residue constitute the active centre of
the peptidase S39 family domain [1,2,3,4].

The peptidase  family  S39 domain consists of two beta barrrels (domains I and
II) connected  by  a long inter-domain loop (see <PDB:1ZYO>). Both the domains
belong to  the all beta class of proteins. There are only three helices in the
peptidase S39  domain  [4].  The  active  site and the substrate-binding cleft
occur in  between  the  two domains and are fairly exposed to the solvent. The
active site  histidine  forms  hydrogen  bonds with both serine and aspartate,
the other two residues of the catalytic triad [4].

The profile we developed covers the entire peptidase family S39 domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: July 2018 / First entry.

[ 1] Revill P.A., Davidson A.D., Wright P.J.
     "Mushroom bacilliform virus RNA: the initiation of translation at the
     5' end of the genome and identification of the VPg."
     Virology 249:231-237(1998).
     PubMed=9791015; DOI=10.1006/viro.1998.9345
[ 2] Sadowy E., Juszczuk M., David C., Gronenborn B., Hulanicka M.D.
     "Mutational analysis of the proteinase function of Potato leafroll
     virus."
     J. Gen. Virol. 82:1517-1527(2001).
     PubMed=11369899; DOI=10.1099/0022-1317-82-6-1517
[ 3] Satheshkumar P.S., Lokesh G.L., Savithri H.S.
     "Polyprotein processing: cis and trans proteolytic activities of
     Sesbania mosaic virus serine protease."
     Virology 318:429-438(2004).
     PubMed=14972568; DOI=10.1016/j.virol.2003.09.035
[ 4] Gayathri P., Satheshkumar P.S., Prasad K., Nair S., Savithri H.S.,
     Murthy M.R.
     "Crystal structure of the serine protease domain of Sesbania mosaic
     virus polyprotein and mutational analysis of residues forming the
     S1-binding pocket."
     Virology 346:440-451(2006).
     PubMed=16356524; DOI=10.1016/j.virol.2005.11.011
[E1] https://viralzone.expasy.org/164
[E2] https://viralzone.expasy.org/45
[E3] https://viralzone.expasy.org/177
[E4] https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=S39

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