{PDOC51690}
{PS51690; ALPHAVIRUS_CP}
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* Alphavirus core protein (CP) domain profile *
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Togaviruses are  enveloped  animal  viruses  containing a single-stranded RNA-
genome of  positive  polarity [E1]. They can cause a variety of diseases, such
as encephalitis,  fever,  arthritis  and  rash.  Togaviruses of the alphavirus
group consist  of  a  nucleoprotein  core,  a  lipid  membrane  bilayer  which
envelopes the  core,  and  glycoprotein spikes on the surface of the membrane.
The core  contains the genomic RNA and the core protein (CP). CP is located at
the N-terminal  end  of  the viral structural polyprotein, which is translated
from a  subgenomic  RNA.  It is followed in the polyprotein by the E3-E2-6K-E1
proteins. At  the  first  step  in  the  post-translational processing of this
polyprotein, CP  acts  as a cis proteinase to auto-catalytically cleave itself
from the  rest  of the polyprotein. Biologically CP functions as a proteolytic
enzyme only  once,  in  the  auto-catalytic  cleavage at Trp. Thereafter it is
auto-inhibited by  the presence of the Trp side-chain in the substrate-binding
pocket [1,2,3]. The alphavirus CP forms peptidase family S3 [2,E2].

The polypeptide  backbone  fold  of  CP is similar to that of the chymotrypsin
family of  serine  proteinases.  The  structure consists of two similar "Greek
key" beta-barrel  sub-domains, formed with the N- and the C-terminal halves of
the protein  (see <PDB:2SNV>). The active site is in a cleft between these two
sub-domains. Ser, His and Asp form the catalytic triad. The aminoacid sequence
Gly-Asp-Ser-Gly, which  is  conserved  among  all the chymotrypsin-like serine
proteases and  contains  the catalytically essential Ser is also present in CP
[1,2,3].

The profile we developed covers the entire alphavirus CP domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: October 2013 / First entry.

[ 1] Choi H.-K., Tong L., Minor W., Dumas P., Boege U., Rossmann M.G.,
     Wengler G.
     "Structure of Sindbis virus core protein reveals a chymotrypsin-like
     serine proteinase and the organization of the virion."
     Nature 354:37-43(1991).
     PubMed=1944569; DOI=10.1038/354037a0
[ 2] Tong L., Wengler G., Rossmann M.G.
     "Refined structure of Sindbis virus core protein and comparison with
     other chymotrypsin-like serine proteinase structures."
     J. Mol. Biol. 230:228-247(1993).
     PubMed=8450538; DOI=10.1006/jmbi.1993.1139
[ 3] Lee S., Owen K.E., Choi H.-K., Lee H., Lu G., Wengler G., Brown D.T.,
     Rossmann M.G., Kuhn R.J.
     "Identification of a protein binding site on the surface of the
     alphavirus nucleocapsid and its implication in virus assembly."
     Structure 4:531-541(1996).
     PubMed=8736552
[E1] https://viralzone.expasy.org/3?outline=all_by_species
[E2] https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=s3

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