{PDOC51920}
{PS51920; SARS_9B}
{BEGIN}
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* Sarbecovirus 9b domain profile *
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Coronaviruses are  enveloped  positive-strand  RNA  viruses  that  infect many
species, including humans, other mammals, and birds [E1]. After infection, the
host may   develop  respiratory,  bowel,  liver,  and  neurological  diseases.
Coronaviruses are divided into four genera: Alphacoronavirus, Betacoronavirus,
Gammacoronavirus, and  Deltacoronavirus.  SARS,  SARS-CoV-2, BatCoV RaTG13 and
Bat-SARS-like coronavirus  (BATSL-CoVZXC21  and  BAT-SL-CoVZC45) belong to the
Sarbecovirus subgenus of Betacoronavirus.

Coronaviruses code  for  the  characteristic  proteins  replicase  polyprotein
(pp1ab), spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins.
In addition, Sarbecoviruses code for subgroup-specific accessory proteins that
are thought  to  be dispensable for viral replication in cell culture, but may
be important  for  virus-host  interactions  and thus contribute to the virus’
fitness.

To achieve  the greatest output from their limited genomes, viruses frequently
make use of alternative open reading frames, in which translation is initiated
from a start codon within an existing gene and, being out of frame, gives rise
to a  distinct  protein  product.  Orf-9b is an alternative open reading frame
within the  nucleocapsid  (N)  gene  from Sarbecoviruses. It codes for a small
accessory protein  of  98  amino-acid residues, which is found in Sarbecovirus
infected cells.  The  orf9b  protein (p9b) has been shown to self-interact and
interact with  nsp5,  nsp14, and the accessory protein p6. The function of p9b
is unknown, although it has been suggested that it specifically recognizes and
binds to  intracellular vesicular membranes. p9b could have a role in membrane
interactions during the assembly of the virus [1,2,3].

The 9b  domain  has a fold with seven beta-strands (see <PDB:2CME>). The beta-
strands from two molecules form two adjacent twisted beta-sheets, resulting in
a highly  interlocked  handshake structure that contains a hydrophobic central
cavity, which binds lipid and stabilizes the molecule [1].

The profile we developed covers the entire Sarbecovirus 9b domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: March 2020 / First entry.

[ 1] Meier C., Aricescu A.R., Assenberg R., Aplin R.T., Gilbert R.J.C.,
     Grimes J.M., Stuart D.I.
     "The crystal structure of ORF-9b, a lipid binding protein from the
     SARS coronavirus."
     Structure 14:1157-1165(2006).
     PubMed=16843897; DOI=10.1016/j.str.2006.05.012
[ 2] Liu D.X., Fung T.S., Chong K.K., Shukla A., Hilgenfeld R.
     "Accessory proteins of SARS-CoV and other coronaviruses."
     Antiviral. Res. 109:97-109(2014).
     PubMed=24995382; DOI=10.1016/j.antiviral.2014.06.013
[ 3] Shukla A., Hilgenfeld R.
     "Acquisition of new protein domains by coronaviruses: analysis of
     overlapping genes coding for proteins N and 9b in SARS coronavirus."
     Virus. Genes. 50:29-38(2015).
     PubMed=25410051; DOI=10.1007/s11262-014-1139-8
[E1] https://viralzone.expasy.org/30?outline=all_by_species

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