Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis

Abstract

To date, an effective therapeutic treatment that confers strong attenuation toward coronaviruses (CoVs) remains elusive. Of all the potential drug targets, the helicase of CoVs is considered to be one of the most important. Here, we first present the structure of the full-length Nsp13 helicase of SARS-CoV (SARS-Nsp13) and investigate the structural coordination of its five domains and how these contribute to its translocation and unwinding activity. A translocation model is proposed for the Upf1-like helicase members according to three different structural conditions in solution characterized through H/D exchange assay, including substrate state (SARS-Nsp13-dsDNA bound with AMPPNP), transition state (bound with ADP-AlF4−) and product state (bound with ADP). We observed that the β19–β20 loop on the 1A domain is involved in unwinding process directly. Furthermore, we have shown that the RNA dependent RNA polymerase (RdRp), SARS-Nsp12, can enhance the helicase activity of SARS-Nsp13 through interacting with it directly. The interacting regions were identified and can be considered common across CoVs, which provides new insights into the Replication and Transcription Complex (RTC) of CoVs.

Emerging coronaviruses: Genome structure, replication, and pathogenesis

“…Cofactor with nsp7 and nsp12, primase [28][29][30] nsp9 Dimerization and RNA binding 31,32 nsp10 Scaffold protein for nsp14 and nsp16 [33][34][35][36] nsp11 Unknown 37 nsp12 Primer dependent RdRp 28,38,39 nsp13 RNA helicase, 5′ triphosphatase [40][41][42] nsp14 Exoribonuclease, N7-MTase 12,[43][44][45] nsp15 Endoribonuclease, evasion of dsRNA sensors [46][47][48] nsp16 2′-O-MTase; avoiding MDA5 recognition, negatively regulating innate immunity 34,35,49 Abbreviations: 3CL pro , chymotrypsin-like protease; DMV, double-membrane vesicle; dsRNA, double-stranded RNA viruses; IFN, interferon; mRNA, messenger RNA; M pro , main protease.…”

A high ATP concentration enhances the cooperative translocation of the SARS coronavirus helicase nsP13 in the unwinding of duplex RNA

“…Eventually, a conformational change in the helicase is caused upon ATP binding. Upon ATP hydrolysis and/or ADP and phosphate release, the helicase relaxes to the initial conformation, resulting in coordinated domain opening and translocation of the helicase 56 . Therefore, the closed state of helicase is populated upon ATP binding, and the open state is populated when the ATPase products dissociate.…”

When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses

“…This helicase contains a 19-20 loop on 1A domain, which is primarily responsible for its unwinding activity. Furthermore, the study revealed an important interaction of Nsp12 with Nsp13 that further enhances its helicase activity [153].…”

“…Recombinant viral helicase expressed in E.coli Rosetta 2 strain was reported to unwind ~280 bp per second [152]. Figure 30D represents a 2.8 Å X-ray crystal structure of Human SARS Nsp13 (PDB ID: 6JYT) [153]. This helicase contains a 19-20 loop on 1A domain, which is primarily responsible for its unwinding activity.…”