User:Bruna Oliveira de Almeida/Sandbox 1
From Proteopedia
SARS-CoV-2 RNA-dependent RNA polymerase
IntroductionThe RNA dependent RNA polymerase (RdRp) of SARS-CoV-2 (also known as nsp12), which is responsible for a major outbreak of the disease called Coronavirus Disease 2019 (COVID-19), declared pandemic by WHO in 11 march 2020 [1] is an enzyme that catalyzes the synthesis of RNA of the virus SARS-CoV-2 [2](2). This virus belongs to the betacoronavirus genus[3](Zhou et al. 2020) and has a single stranded positive-sense RNA genome. Therefore, RNA dependent RNA polymerase plays a central role in the virus replication and livecycle. It’s also has been considered a good target for antiviral drugs [2](2).
Function The RdRp is responsible for replication and transcription of the virus genome alongside with other non-structural proteins (NSPs). After the firsts stages of infection, follow by the translation and assembly of the replicase complex, this enzyme helps the synthesis of genomic and sub-genomic RNA. Sub-genomic RNAs are used as mRNA for structural and accessory proteins [4](4). The RdRp synthesizes negative-sense RNA and uses it as template for positive-sense strands for RNA replication for packaging into virus particles, and sub-genomic RNA transcription for translation [5](Lai and Cavanagh 1997). Moreover, it has been reported that RdRp gets complex with two other non-structural proteins NSP7 and NSP8, which act as cofactors and confer processivity to its RNA-synthesizing activity [6][7](Zhai et al. 2005, 7). StructureOverviewThe RdRp bonded to NSP7 and NSP8 consists of an approximately 160 kDa protein complex [8](8). The RNA dependent RNA polymerase of SARS-CoV-2 contains 942 amino acid residues while NSP7 has 198 and NSP8 83 residues. (To view the primary and secondary structure of SARS-CoV-2 RdRp and its cofactors visit https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=6m71). The structure of RdRp protein of COVID-19 virus contains four domains: a “right hand” RdRp domain (residues S367-F920), a nidovirus-unique N-terminal extension domain (residues D60-R249), which has a nidovirus RdRp-associated nucleotidyltransferase domain (NiRAN) architecture, an interface domain (residues A250-R365) that connects the RdRp domain and NiRAN domain, and a newly identified β-hairpin domain at its N terminus (residues D29-K50)[2] (2). RdRp domainThe RdRp domain has a conserved architectures and comprises three subdomains: a fingers subdomain (residues L366-A581 and K621-G679), a palm subdomain (residues T582-P620 and T680-Q815), and a thumb subdomain (residues H816-E920)[2] (2). Its active site consists of the polymerase motifs A, B, C, D, E, F, and G, with important catalytic residues (759-SDD-761) been located in Motif C[2] (2). As in other viral RNA polymerases [9](9), the template-directed RNA synthesis is mediated by the RdRp domain motifs[2] (2). NiRAN and β-hairpin domainThe complete SARS-CoV-2 RdRp protein structure obtained by cryo-EM[2](2,10) [10] allowed to resolve the N-terminal portion of the NiRAN domain as well to identify a N-terminal β-hairpin domain, what was in part unresolved for SARS-CoV RdRp protein [8] (8). It was found that this β-hairpin is inserted in the groove clamped by the NiRAN domain and the palm subdomain and it forms close contacts that help to stabilize the overall structure[2] (2). An attractive drug targetAs has been shown, SARS-CoV-2 RdRp protein is crucial for viral replication and so, it has been an important drug target in the fight against COVID-19[2][11] (2,11). In fact, growing attention has been given to RdRp as target of a class of antiviral drugs known as nucleotide analogs, including Remdesivir[10][12] (10,12). Remdesivir is an adenosine monophosphate analog and it is converted into its active drug form (its triphosphate form) within the cells[13] (13). It is positioned at the center of the catalytic active site and, as for other nucleotide analogs, Remdesivir was shown to inhibits the RdRp activity through non-obligate RNA chain termination, which requires the conversion of its monophosphate form to the triphosphate one[10] (10). In a recent study[10] (10), it was described some differences between the apo and the complex (with Remdesivir and a template RNA) structures, showing some small conformational changes between them. (The three dimensional structure of the nsp12-nsp7-nsp8 complex bounded to the template-primer RNA and triphosphate form of Remdesivir can be seen in https://www.rcsb.org/3d-view/7BV2). References
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