Molecule of the Month: SARS-CoV-2 RNA-dependent RNA Polymerase

Coronaviruses duplicate their RNA genome using a specialized polymerase

SARS-CoV-2 RNA-directed RNA polymerase (nsp12) with nsp7 and nsp8, and a short duplex of RNA with a template strand and a product strand. Nsp7 and 8 are removed on the right to show the interaction with RNA.
SARS-CoV-2 RNA-directed RNA polymerase (nsp12) with nsp7 and nsp8, and a short duplex of RNA with a template strand and a product strand. Nsp7 and 8 are removed on the right to show the interaction with RNA.
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Some viruses, including poliovirus, rhinovirus, and coronaviruses, don't bother with DNA at all. They transmit their genetic information as a strand of RNA that can be used as a messenger RNA to build proteins as soon as the virus infects a cell. One of the tricks, however, is that these viruses need a special polymerase that goes against the standard DNA-to-RNA-to-protein information flow. This polymerase makes a new RNA strand using RNA, not DNA, as the template. So, the virus simply needs to encode this polymerase in its RNA genome. Then, the polymerase is made by cellular ribosomes soon after infection and it starts replicating the viral RNA to make new viruses.

Under the Microscope

Amazingly, only a few months after SARS-CoV-2 was discovered, researchers are revealing the structure its RNA-dependent RNA polymerase and exploring its interactions with RNA. Cryoelectron microscopy is being used to determine the structures of the polymerase and its helper proteins, along with small pieces of RNA. A few of the first structures can be found in PDB entries 6yyt (shown here), 7c2k, 7bzf, 7bv2, and 6x2g. These structures include the polymerase (also known as nsp12 for "non-structural protein 12") along with two other viral proteins, nsp7 and nsp8, that help the polymerase stay on track and copy long portions of the RNA chain.

Perfect Target

Since our own cells don't make RNA from RNA, this polymerase is an attractive target for antivirals. New drugs usually take a long time to perfect since they have to be evaluated for effectiveness and safety, but investigational polymerase-targeting agents like remdesivir are being repurposed in the fight against COVID19. Remdesivir was developed to fight hepatitis and Ebola, but wasn't very effective. It is currently approved for emergency use against SARS-CoV-2.
Complex of SARS-CoV nsp7 and nsp8.
Complex of SARS-CoV nsp7 and nsp8.
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Getting Started

Nsp 7 and 8 assist the polymerase in its job, but they are also thought to help get the whole process started by creating a primer at the start of the RNA chain. This structure (PDB entry 2ahm) shows a large, circular complex of SARS-CoV nsp7 and nsp8 composed of 16 chains. Researchers have speculated that it encircles the RNA strand and creates the primer. It is currently unknown if something similar occurs with SARS-CoV-2.

Exploring the Structure

RNA-dependent RNA Polymerase

Remdesivir is a modified adenine-like nucleotide that is converted to an active triphosphate form and then added to the product RNA strand, blocking the function of the polymerase. This structure (PDB entry 7bv2) captures the drug (green) after it has been attached to the product strand. Two magnesium ions (magenta) assist with the normal polymerase reaction, and the structure also found a pyrophosphate nearby (dark purple). To explore this structure in more detail, click on the image for an interactive JSmol.

Topics for Further Discussion

  1. Try searching for "RNA-dependent RNA polymerase" at the main RCSB site to see similar enzymes from other viruses.
  2. Be sure to take a look at the cryoEM maps for these structures at the EMDataBank--there is a link to them at the top of each Structure Summary page.

Related PDB-101 Resources

References

  1. 6yyt: Hillen, H.S., Kokic, G., Farnung, L., Dienemann, C., Tegunov, D., Cramer, P. (2020) Structure of replicating SARS-CoV-2 polymerase. Nature, https://doi.org/10.1038/s41586-020-2368-8
  2. 7c2k, 7bzf, : Wang, Q., Wu, J., Wang, H., Gao, Y., Liu, Q., Mu, A., Ji, W., Yan, L., Zhu, Y., Zhu, C., Fang, X., Yang, X., Huang, Y., Gao, H., Liu, F., Ge, J., Sun, Q., Yang, X., Xu, W., Liu, Z., Yang, H., Lou, Z., Jiang, B., Guddat, L.W., Gong, P., Rao, Z. (2020) Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase. Cell 182: 1-12.
  3. 7bv2: Yin, W., Mao, C., Luan, X., Shen, D.D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.C., Tian, G., Jiang, H.W., Tao, S.C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., Zhang, S., Zhang, Y., Xu, H.E. (2020) Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science 368: 1499-1504.
  4. 2ahm: Zhai, Y.J., Sun, F., Li, X., Pang, H., Xu, X., Bartlam, M., Rao, Z. (2005) Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer. Nat Struct Mol Biol 12: 980-986.

September 2020, David Goodsell

http://doi.org/10.2210/rcsb_pdb/mom_2020_9
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More