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PROSITE documentation PDOC51920

Sarbecovirus 9b domain profile





Description

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: αcoronavirus, βcoronavirus, γcoronavirus, and Deltacoronavirus. SARS, SARS-Co-2V, BatCoV RaTG13 and Bat-SARS-like coronavirus (BATSL-CoVZXC21 and BAT-SL-CoVZC45) belong to the Sarbecovirus subgenus of βcoronavirus.

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 β-strands (see <PDB:2CME>). The β-strands from two molecules form two adjacent twisted β-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.

Last update:

March 2020 / First entry.

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Technical section

PROSITE method (with tools and information) covered by this documentation:

SARS_9B, PS51920; Sarbecovirus 9b domain profile  (MATRIX)


References

1AuthorsMeier C. Aricescu A.R. Assenberg R. Aplin R.T. Gilbert R.J.C. Grimes J.M. Stuart D.I.
TitleThe crystal structure of ORF-9b, a lipid binding protein from the SARS coronavirus.
SourceStructure 14:1157-1165(2006).
PubMed ID16843897
DOI10.1016/j.str.2006.05.012

2AuthorsLiu D.X. Fung T.S. Chong K.K. Shukla A. Hilgenfeld R.
TitleAccessory proteins of SARS-CoV and other coronaviruses.
SourceAntiviral. Res. 109:97-109(2014).
PubMed ID24995382
DOI10.1016/j.antiviral.2014.06.013

3AuthorsShukla A. Hilgenfeld R.
TitleAcquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus.
SourceVirus. Genes. 50:29-38(2015).
PubMed ID25410051
DOI10.1007/s11262-014-1139-8

E1Titlehttps://viralzone.expasy.org/30?outline=all_by_species



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