PROSITE documentation PDOC51989

Coronavirus (CoV) Nsp2 N-terminal, middle and C-terminal domains profiles

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: αcoronavirus, βcoronavirus, γcoronavirus, and Deltacoronavirus. The ideal hosts of αCoV and βCoV are mammals, and γCoV primarily infects birds, while DeltaCoV has been identified in both mammals and birds. SARS, SARS-CoV-2, BatCoV RaTG13 and Bat-SARS-like coronavirus (BATSL-CoVZXC21 and BAT-SL-CoVZC45) belong to the Sarbecovirus subgenus of βCoV [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) that fulfill a number of essential viral functions including RNA replication, replication proofreading, double-membrane vesicle formation, and others. Many of these also interact with host factors to effectively subvert the host cell to meet the virus’s needs. Such subversion, for example, includes suppressing host innate immune responses, host translation, nuclear import, and other effects. Although Nsp2 is present in SARS-CoV-1, CoV-2, MERS-and in closely related coronaviruses in bats, pangolins and other animals-there is a considerable sequence variation across different species. This degree of variability may indicate rapid Nsp2 adaptation under host-specific selection pressures. Nsp2 has been implicated in processes ranging from translation repression to endosomal transport, ribosome biogenesis, and actin filament binding. Nsp2 in SARS-CoV-2 and other coronaviruses have been observed to localize to endosomes and replication-transcription complexes (RTC). Nsp2 may be involved in binding nucleic acids and regulating intracellular signaling pathways. It contains an N-terminal, a middle and a C-terminal domain [1,2].

The Nsp2 N-terminal domain contains ten α-helices (α1-α10) and fourteen β-sheets (β1-β14) with three zinc fingers (ZnFs), belonging to the C2H2, C4, and C2HC types, respectively (see <PDB:7EXM>). The three zinc fingers are not involved in binding nucleic acids directly but may play other unknown functions. The interaction of Nsp2 and nucleic acid is mainly dependent on a large positively charged region on the electrostatic surface of the Nsp2 N-terminal domain [2].

The profiles we developed cover respectively the entire CoV Nsp2 N-terminal, middle and C-terminal domains.