SARS-CoV-2 protein NSP8

Function

Two different conformations of nsp8 and one nsp7 work as a co-factor for nsp12. Together, these four proteins form the minimal core polymerase complex. Without its co-factors nsp12 has a low efficiency in polymerase activity. This complex plays a key role in RNA synthesis of the virus, making it an important player in the replication procedure^[1]. It has been suggested that the nsp7-nsp8 dimer might act as a primase in the complex^[2].

Disease

The global COVID-19 pandemic, which started in 2019, is caused by the SARS-CoV-2.

Structure

The nsp8 is encoded on the open reading frame ORF1a, contains 198 amino acids^[2] and has two subdomains. The first domain has an α-turn-α motif (α1: E77-L98 and α2: D101-D112). The second domain has four antiparallel β-strands consisting the C-terminal subdomain (β1: A125-I132, β2: T146-Y149, β3: A152- V160, β4: L184-R190) with an inserted α3 (Y135-T141) ^[2]. Depending on whether the nsp8 (nsp8.1) forms a dimer with nsp7 to bind to nsp12 or binds as a monomer (nsp8.2) to nsp12, it forms significantly different conformations. The N-terminal extension helix shows substantial refolding^[1].

The nsp7-nsp8.1 heterodimer binds to nsp12 above the thumb domain of the RNA-dependent RNA polymerase (RdRp), mostly mediated by nsp7. With this interaction, the conformation of the finger extension loops of the nsp12 are stabilized^[1]. The dimerization interface of the nsp7-nsp8 heterodimer has an area of 1340 Ų and is formed by the α1 and α2 of nsp8 and the α1 and α3 helices of nsp7^[2].

The nsp8.2 monomer forms interactions with the top region of the finger subdomain and the interface domain of nsp12.

A prominent feature of both nsp8 subunits are the long α-helical extensions up to 28 base pairs away from the active site. The residues of the RdRp flanking the exiting RNA are positively charged. These only become ordered when interacting with the exiting RNA duplex^[3].

Variations

Compared to the amino acid sequence of SARS-CoV, the SARS-CoV-2 sequence has five amino acid substitutions, resulting in a sequence identity of 97.5%^[4]. Even though these substitutions do not result in apparent structural changes, a study showed a 35% lower efficiency for the RdRp complex compared to SARS-CoV^[1]. A cross-combination analysis showed that replacing the nsp8 subunits in the SARS-CoV-2 polymerase complex by its SARS-CoV homologue increases the activity by ~2.1 times. Further, the melting temperature of the nsp8 subunit of SARS-CoV-2 is shown to be lower than for SARS-CoV^[1].

See also

Coronavirus_Disease 2019 (COVID-19)
SARS-CoV-2_virus_proteins
COVID-19 AlphaFold2 Models