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PROSITE documentation PDOC51948

Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) and Nsp7 and Nsp8 cofactors 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. 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 them, the Nsp12 RNA-dependent RNA polymerase, that includes an RdRp catalytic domain conserved in all RNA viruses (see <PDOC50507>), possesses some minimal activity on its own, but the addition of the Nsp7 and Nsp8 cofactors greatly stimulates polymerase activity. The Nsp12-Nsp7-Nsp8 subcomplex is thus defined as the minimal core component for mediating coronavirus RNA synthesis. To achieve complete transcription and replication of the viral genome, several other Nsp subunits are required to assemble into a holoenzyme complex, including Nsp10, Nsp13, Nsp14 and Nsp16 [1,2,3,4,5].

The CoV polymerase complex consists of a Nsp12 core catalytic subunit bound with a Nsp7-Nsp8 heterodimer and an additional Nsp8 subunit at a different binding site. The Nsp12 subunit contains an N-terminal NiRAN domain (see <PS51947>), an interface domain and a C-terminal polymerase domain, which resembles a right hand, comprising the fingers, palm and thumb subdomains (see <PDB:6YYT>). The active site is located on the palm subdomain and is formed by five conserved Nsp12 elements known as motifs A-E. Motif C binds to the RNA 3' end and contains the catalytic residues (SDD), which are required for RNA synthesis and reside in a β-turn loop connecting two adjacent strands. The additional Nsp12 motifs F and G reside in the fingers subdomain and position the RNA template [2,3,4,5].

An Nsp7-Nsp8 heterodimer binds to the thumb, and an additional copy of Nsp8 binds to the fingers subdomain. Nsp7 is an all-α-helical protein (see <PDB:2AHM; C>). Its central core is an N-terminal helical bundle (HB), with helices HB1, HB2 and HB3, forming a triple-stranded antiparallel coiled coil with a right-handed superhelical pitch. The Nsp8 cofactor domain, which has a proposed primase or 3'-terminal adenylyltransferase activity, has a 'golf club'-like structure composed of a long α-helix N-terminal 'shaft' subdomain and an α/β C-terminal 'head' subdomain (see <PDB:2AHM; H>). The shaft subdomain contains three helices. Another three α-helices and seven β-strands form the head domain, which has an α/β fold. The seven β-strands form an open-barrel with two antiparallel β-sheets packed orthogonally. More than half the residues in the C-terminal domain are hydrophobic, and the whole domain forms a tight hydrophobic core [6,7,8].

The profiles we developed cover the entire CoV Nsp12 RNA-dependent RNA polymerase and Nsp7 and Nsp8 cofactors domains.

Last update:

December 2020 / First entry.


Technical section

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

COV_NSP12_RDRP, PS51948; Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile  (MATRIX)

COV_NSP7, PS51949; Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile  (MATRIX)

COV_NSP8, PS51950; Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile  (MATRIX)


1AuthorsV'kovski P. Kratzel A. Steiner S. Stalder H. Thiel V.
TitleCoronavirus biology and replication: implications for SARS-CoV-2.
SourceNat. Rev. Microbiol. 0:0-0(2020).
PubMed ID33116300

2AuthorsGao Y. Yan L. Huang Y. Liu F. Zhao Y. Cao L. Wang T. Sun Q. Ming Z. Zhang L. Ge J. Zheng L. Zhang Y. Wang H. Zhu Y. Zhu C. Hu T. Hua T. Zhang B. Yang X. Li J. Yang H. Liu Z. Xu W. Guddat L.W. Wang Q. Lou Z. Rao Z.
TitleStructure of the RNA-dependent RNA polymerase from COVID-19 virus.
SourceScience 368:779-782(2020).
PubMed ID32277040

3AuthorsPeng Q. Peng R. Yuan B. Zhao J. Wang M. Wang X. Wang Q. Sun Y. Fan Z. Qi J. Gao G.F. Shi Y.
TitleStructural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.
SourceCell. Rep. 31:107774-107774(2020).
PubMed ID32531208

4AuthorsHillen H.S. Kokic G. Farnung L. Dienemann C. Tegunov D. Cramer P.
TitleStructure of replicating SARS-CoV-2 polymerase.
SourceNature 584:154-156(2020).
PubMed ID32438371

5AuthorsWakchaure P.D. Ghosh S. Ganguly B.
TitleRevealing the Inhibition Mechanism of RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2 by Remdesivir and Nucleotide Analogues: A Molecular Dynamics Simulation Study.
SourceJ. Phys. Chem. B. 124:10641-10652(2020).
PubMed ID33190493

6AuthorsJohnson M.A. Jaudzems K. Wuethrich K.
TitleNMR Structure of the SARS-CoV Nonstructural Protein 7 in Solution at pH 6.5.
SourceJ. Mol. Biol. 402:619-628(2010).
PubMed ID20709084

7AuthorsZhai Y. Sun F. Li X. Pang H. Xu X. Bartlam M. Rao Z.
TitleInsights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer.
SourceNat. Struct. Mol. Biol. 12:980-986(2005).
PubMed ID16228002

8AuthorsImbert I. Guillemot J.-C. Bourhis J.-M. Bussetta C. Coutard B. Egloff M.-P. Ferron F. Gorbalenya A.E. Canard B.
TitleA second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus.
SourceEMBO. J. 25:4933-4942(2006).
PubMed ID17024178


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