SARS-CoV-2 protein NSP14

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

To the right is an AlphaFold2 3D model of SARS CoV-2 Protein NSP14 (length = 527 amino acids, NCBI ID QHD43415_13) color coded by the pLDDT scores. It corresponds to the highest ranked model in terms of the pLDDT confidence scores, i.e., model 4^[1].

Morph of the top 5 ranked AlphaFold2 models of SARS-CoV-2 Protein NSP11, rainbow color coded N-C (blue to red)^[1].

Function

Nsp14 is an enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity ^[2][3]. Nsp14 is translated as part of the polyprotein pp1ab. This polyprotein is subsequently processed by the Main protease (SARS-CoV-2_Coronavirus_Main_Protease) and Papain-like protease (SARS-CoV-2_enzyme_Papain-like) into individual functional proteins. Nsp14 is a multidomain protein made up of 527 residues^[2][3].

The exoribonuclease (ExoN) domain of Nsp14 has a DEEDh motif like the DEDD motif described in other ExoN enzymes^[4]. This active site along with the zinc binding sites are required for ExoN activity^[5][6]. The interaction of Nsp10 with Nsp14 has an allosteric effect on ExoN activity, increasing activity by 35-fold^[5][7]. Without this interaction the active site is thought to be left wide open with lower affinity for substrates^[5]. This domain provides a proofreading function allowing high fidelity reproduction of RNA^[7][8]. It is thought this ExoN activity allows Coronaviruses to have such a large genome of ~30 kb, where viruses lacking this activity have genomes of less than 20 kb^[8]

The Guanine-N7-methyltransferase (N7-MTase) domain does not have a Rossmann fold usually seen in methyltransferase enzymes^[5][6]. This N7-MTase domain performs the first 5’ methylation of the GpppA cap providing efficient RNA translation and protection from the hosts innate immune system^[9].

Disease

SARS-CoV-2 is the cause of a global COVID-19 pandemic which started in 2019.

Relevance

SARS-CoV-2 Non-structural protein 14 (Nsp14) represents a potential drug target for treatment of COVID-19. As Nsp14 has two domains with different activities, both the Exoribonuclease and the N7-guanine methyltransferase activity could be of interest for drug targets.

Structural highlights

The structure and function of Nsp14 is thought to be the similar between SARS-CoV and SARS-CoV-2 based on the sequence identity of 95% between viruses.

Nsp14 has two distinct domains with the N-terminal domain having exoribonuclease activity (residues 1-287). The secondary structure of the ExoN domain consists of 6 α-helices, and 10 β-strands that make up three distinct β-sheets. The centre of the domain is formed by an antiparallel β-sheet (β10, β7, β2, β3, and β4) surrounded by five α-helices (α1, α2, α3, α4, and α6). This central region contains the DEEDh motif responsible for exonuclease activity (Asp90, Glu92, Glu191, His268, and Asp273). The third distinct β-sheet leads from the base of the central region of α4 and β10. This sheet is formed by β9 and β8 with the first zinc finger motif found in the ExoN domain (Cys207, Cys210, Cys226, and His229). The second zinc finger motif is coordinated between α5 and α6 (His257, Cys261, His264, and Cys279). These two zinc fingers are required for ExoN activity. Nsp14 forms a heterodimer with Nsp10 through the N-terminus of its ExoN domain. The Nsp10 interface found in Nsp14 is coordinated with an antiparallel β-sheet (β1, β5, and β6). The Nsp10/Nsp14 interaction surface is 7,798 Å^2 in size.

A flexible hinge region connects the ExoN domain to the C-terminal domain that has an N7-MTase activity (residues 288-527). The hinge region connecting the two domains is made of an antiparallel β-sheet found at the centre of the domains sequence (β18, β17, and β16). The N7-MTase domain consists of 12 β-strands and 5 α-helices. The central β-sheet has four parallel strands (β12, β11, β14, and β15) and one antiparallel (β22). The binding pocket for the two functional ligands SAH and GpppA (PDBID: 5c8s)are found at one end of the central β-sheet. SAH binding involves the residues Trp292, Asp331, Gly333, Pro335, Lys336, Asp352, and Val389. The binding of GpppA involves the residues Arg310, Trp385, Asn386, Phe410, Leu419, Tyr420, Asn422, Lys423, Phe426, Thr428, Phe506, Thr428, and Phe506. The last zinc binding finger (Cys452, Cys477, Cys484, and His487) is located near the C-terminus of the protein coordinated with the final long α-helix (α9).

All the above structural information was taken from publications on the structures currently available for SARS-CoV (PDBID: 5c8s, 5c8t, 5c8u, and 5nfy) ^[5][6] as no SARS-CoV-2 structures are currently available.

See also

Coronavirus_Disease 2019 (COVID-19)