SARS-CoV-2 (2019nCoV, novel Coronavirus)Non-structure protein (Nsp1-Nsp16)

1. Nsp3: Nsp3 (200 kDa) is the largest protein encoded by the coronavirus (CoV) genome. Nsp3 is an essential component of the replication and transcription complex. It comprises various domains, the organization of which differs between CoV genera, due to duplication or absence of some domains. However, the N-terminal region of the Nsp3 is highly conserved among CoV, containing a ubiquitin-like (Ubl) globular fold followed by a flexible, extended acidic-domain (AC domain) rich in glutamic acid (38%). Next to the AC domain is a catalytically active ADP-ribose-1″-phosphatase (ADRP, app-1″-pase) domain (also called macro domain or X domain) thought to play a role during synthesis of viral subgenomic RNAs. SARS Unique Domain (SUD), a domain not yet identified in other coronaviruses from alphacoronavirus and betacoronavirus, follows next. The SUD domain binds oligonucleotides known to form G-quadruplexes. Downstream of the SUD domain is a second Ubl domain and the catalytically active PLpro domain that proteolytically processes the Nsp1/2, Nsp2/3 and Nsp3/4 cleavage sites. Downstream of PLpro are found a nucleic acid-binding domain (NAB) with a nucleic acid chaperon function, which is conserved in betacoronavirus and gammacoronavirus, and one uncharacterized domain termed the marker domain (G2M). Following the G2M are two predicted double-pass transmembrane domains (TM1–2 and TM3–4), a putative metal binding region (ZN) and the Y domain of unknown function (subdomains Y1–3).

2. Nsp5: Nsp5 protease (3CLpro; Mpro) mediates processing at 11 distinct cleavage sites, including its own autoproteolysis, and is essential for virus replication. Nsp5 exhibits a conserved three-domain structure and catalytic residues.

3. Nsp10: Nsp10 (18 kDa) is well conserved among coronaviruses and encoded by ORF1a. It’s thought to serve as an important multifunctional cofactor in replication. Nsp10 was shown to interact with itself, as well as with Nsp1, Nsp7, Nsp14, and Nsp16. The important role of Nsp10 is responsible for RNA synthesis. It was shown that a murine hepatitis virus (MHV) temperature-sensitive mutant carrying a non-synonymous mutation in the Nsp10 coding sequence had a defect in minus-strand RNA synthesis at non-permissive temperatures.

4. Nsp12: Nsp12 (102 kDa) is a multidomain RNA polymerase, which is the most conserved protein in coronaviruses. Nsp12 contains an RNA-dependent RNA polymerase (RdRp) domain in its C-terminal, which is essential for the viral replication and transcription.

5. Nsp16: Nsp16 is an SAM-dependent nucleoside-2’O-methyl-transferase (2’O-MTase). The mRNA cap for coronaviruses is completed by Nsp16, which ensures formation of a protective cap-1 structure that prevent recognition by either MDA5 or IFIT proteins. Finally, the NSP16/NSP10 complex finishes coronavirus capping process permitting viral infection with reduced host recognition.