RdRp catalytic domain of RNA-directed RNA polymerase

General information on RdRp catalytic domain of RNA-directed RNA polymerase

RNA-dependent RNA polymerases (RdRp) also known as nonstructural protein 12(nsp12) is essential for genomic replication and is found in positive-sense RNA viruses. In the case of coronavirus (CoV), a large nidovirus subtype, viral RNA depends on RdRps complex to control nucleotide fidelity and selectivity. CoV can cause disease in mammals and birds. In humans, the virus is responsible for coronavirus disease (COVID) and can affect respiratory epithelial cells which cause respiratory tract infections. COVID virus are the only known viruses to have replicase proteins that regulate genomic fidelity as well as proofreading exonuclease (nsp14). It remains unknown to what degree nsp12 protein participate to replication fidelity. However, it is believed that nsp14 exonuclease is epistatic to nsp12 activity.
RdRp protein contains a polymerase domain which is comprised of a fingers domain, a palm domain and a thumb domain. CoV nsp12 also contains a N-terminal extension which is very specific to nidoviruses. Two metal-binding sites are found in nsp12 structure. The metal-binding sites have zinc atoms assigned and are distally located to known active-sites. As such, it is believed that the metal-binding sites are structural components rather than directly involved in enzymatic activity. Although the outer surface of nsp12 proteins is largely negative, the polymerase RNA template and nucleotide triphosphate binding site (NTP) has a strong positive electrostatic potential. RdRp protein has shown no kinase activity,however, several shared kinases catalytic residues are visible in CoV nsp12 including Asn209 and the conserved Asp218 and Phe219.
Nsp12 bounds to its essential co-factors nonstructural protein 7 (nsp7) and nonstructural protein 8 (nsp8). The large N-terminal domain is linked to two nsp8. The nsp7-nsp8-nsp12 complex formed is believer to represent the minimal complex required for nucleotide polymerization. The presence of structural metal-binding zinc ions in nsp12 protein suggest potential interaction with nsp3, nsp10, nsp13, and nsp14. This points to potential involvement of RdRp protein in protein folding.