{PDOC51994}
{PS51994; BCOV_NSP3E_G2M}
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* Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile *
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Coronaviruses (CoVs)  are  enveloped  positive-strand  RNA viruses that infect
many species, including humans, other mammals, and birds. 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 [E1].

The CoV  replicase  gene encodes two overlapping polyproteins, termed pp1a and
pp1ab, which  mediate  viral  replication  and transcription. The polypeptides
pp1a and  pp1ab  are  processed  by  the action of a main protease (Nsp5) (see
<PDOC51442>) and of one or two papain-like proteases (PLpro) (see <PDOC51124>)
found in  Nsp3  into  non-structural  proteins (Nsps) to form the replication/
transcription complex (RTC). Among these, Nsp3 is a glycosylated, multidomain,
integral membrane  protein.  Nsp3 plays many roles in the viral life cycle. It
can act  as a scaffold protein to interact with itself and to bind other viral
Nsps or  host  proteins.  In  particular, Nsp3 is essential for RTC formation.
Nsp3 comprises  various domains, the organization of which differs between CoV
genera, due  to  duplication  or  absence  of some domains. Nsp3e is unique to
Betacoronaviruses and  consists  of  a  nucleic acid-binding domain (NAB) (see
<PDOC51945>) and    the   so-called   group   2-specific   marker   (G2M)   or
Betacoronavirus-specific marker  (BetaSM).  The corresponding region is absent
in Alphacoronaviruses and Deltacoronaviruses [1,2,3,4],

The Nsp3e G2M domain possesses an alpha/beta fold (see <PDB:7T9W>).

The profile we developed covers the entire Nsp3e G2M domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: January 2021 / First entry.

[ 1] Neuman B.W., Joseph J.S., Saikatendu K.S., Serrano P., Chatterjee A.,
     Johnson M.A., Liao L., Klaus J.P., Yates J.R. III, Wuethrich K.,
     Stevens R.C., Buchmeier M.J., Kuhn P.
     "Proteomics analysis unravels the functional repertoire of coronavirus
     nonstructural protein 3."
     J. Virol. 82:5279-5294(2008).
     PubMed=18367524; DOI=10.1128/JVI.02631-07
[ 2] Neuman B.W.
     "Bioinformatics and functional analyses of coronavirus nonstructural
     proteins involved in the formation of replicative organelles."
     Antiviral. Res. 135:97-107(2016).
     PubMed=27743916; DOI=10.1016/j.antiviral.2016.10.005
[ 3] Lei J., Kusov Y., Hilgenfeld R.
     "Nsp3 of coronaviruses: Structures and functions of a large
     multi-domain protein."
     Antiviral. Res. 149:58-74(2018).
     PubMed=29128390; DOI=10.1016/j.antiviral.2017.11.001
[ 4] Korn S.M., Dhamotharan K., Fuertig B., Hengesbach M., Loehr F.,
     Qureshi N.S., Richter C., Saxena K., Schwalbe H., Tants J.-N.,
     Weigand J.E., Woehnert J., Schlundt A.
     "(1)H, (13)C, and (15)N backbone chemical shift assignments of the
     nucleic acid-binding domain of SARS-CoV-2 non-structural protein 3e."
     Biomol. NMR. Assign. 14:329-333(2020).
     PubMed=32770392; DOI=10.1007/s12104-020-09971-6
[E1] https://viralzone.expasy.org/30?outline=all_by_species

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