PROSITE documentation PDOC51945
Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile


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. SARS, SARS-CoV-2, BatCoV RaTG13 and Bat-SARS-like coronavirus (BATSL-CoVZXC21 and BAT-SL-CoVZC45) belong to the Sarbecovirus subgenus of βcoronavirus [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 of functional and structural importance for virus replication, the organization of which differs between CoV genera, due to duplication or absence of some domains [1]. Nsp3e is unique to βcoronaviruses and consists of a nucleic acid-binding domain (NAB) and the so-called group 2-specific marker (G2M). The Nsp3e NAB was shown to bind G-rich single-stranded RNA (ssRNA) and to possess double-stranded DNA (dsDNA) unwinding capability [2,3,4].

The Nsp3e NAB domain comprises two antiparallel β-sheets and one parallel β-sheet as well as two α-helices and two 3(10)-helices, with the parallel four-strand β-sheet holding the two α-helices that are oriented antiparallel to the β-strands. The two antiparallel two-strand β-sheets and the two 3(10)-helices are anchored against the surface of the barrel-like molecular core formed by the four-strand β-sheet and the two α-helices (see <PDB:2K87>) [3].

The profile we developed covers the entire β-CoV Nsp3e NAB domain.

Last update:

October 2020 / First entry.


Technical section

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

BCOV_NSP3E_NAB, PS51945; Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile  (MATRIX)


1AuthorsLei J. Kusov Y. Hilgenfeld R.
TitleNsp3 of coronaviruses: Structures and functions of a large multi-domain protein.
SourceAntiviral. Res. 149:58-74(2018).
PubMed ID29128390

2AuthorsSerrano P. Johnson M.A. Chatterjee A. Pedrini B. Wuethrich K.
TitleNMR assignment of the nonstructural protein nsp3(1066-1181) from SARS-CoV.
SourceBiomol. NMR. Assign. 2:135-138(2008).
PubMed ID19636888

3AuthorsSerrano P. Johnson M.A. Chatterjee A. Neuman B.W. Joseph J.S. Buchmeier M.J. Kuhn P. Wuethrich K.
TitleNuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3.
SourceJ. Virol. 83:12998-13008(2009).
PubMed ID19828617

4AuthorsKorn 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.
Title(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.
SourceBiomol. NMR. Assign. 14:329-333(2020).
PubMed ID32770392


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