SARS-CoV-2 enzyme Hel: Difference between revisions

Latest revision as of 11:38, 17 February 2021

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution (PDB 6zsl).

Non-structural protein 13 (nsp13)/ Helicase (Hel)

Function

The multifunctional non-structural protein nsp13, also referred to as helicase, contains 601 amino acids^[1] and is encoded on the ORF1b^[2]. It is part of the superfamily 1B^[3] and highly conserved within all coronaviruses^[4].

Nsp13 is a key enzyme of the viral replication that initiates the first step of the RNA cap synthesis. The capping of the viral RNA is essential to protect it from cellular innate immunity attack, to stabilize it and ensure its translation^[5]. The process of installing the type 1 cap (m7GpppNm-RNA) involves the enzymes nsp13, nsp14, nsp16 and nsp10, with nsp10 acting as an allosteric activator for nsp14 and nsp16, and a still unknown GTase^[4]. Here nsp13 works as an RNA 5’-triphosphatase and hydrolyses the 5’ γ-phosphate of the pppN-RNA as the first step of the capping process^[4].

Another function of the nsp13 is the NTP-dependent unwinding of RNA duplexes with a 5’ to 3’ polarity. This activity is stimulated by interaction with nsp12, the RNA-dependent RNA polymerase (RdRp) ^[3]^[4].

Additionally, nsp13 might act as a potent interferon antagonist^[6].

Disease

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

Structure

Compared to the amino acid sequence of SARS-CoV, the SARS-CoV-2 sequence of nsp13 has one amino acid substitution, resulting in a sequence identity of 99.8% and a sequence similarity of 100.0%^[1]. Due to this near perfect match, the nsp13 of SARS-CoV and SARS-CoV-2 share the same structure^[4]. Both show many structural similarities with the eukaryotic Upf1 helicase^[4].

Nsp13 comprises of five domains: The N-terminal Zinc binding domain (ZBD) (amino acids 1-100), the stalk domain (101-150), 1B (151-261), 1A (262-442), and the 2A domain (443-601). The last three have been shown to be responsible for nucleic acid binding and the NTPase activity, while the ZBD and 1A can directly interact with nsp12 to enhance the helicase activity of nsp13. Together they fold in a triangular shape with 1A, 1B and 2A forming the base and the stalk domain and ZBD at the apex^[4]. Nsp13 might form a stable holo-RdRp complex with nsp12, nsp7 and nsp8 by interacting with the nsp8 extensions and the nsp12 thumb domain and may play a role in backtracking^[3].

ReferencesReferences

↑ ^1.0 ^1.1 Yoshimoto FK. The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. Protein J. 2020 Jun;39(3):198-216. doi: 10.1007/s10930-020-09901-4. PMID:32447571 doi:http://dx.doi.org/10.1007/s10930-020-09901-4
↑ Konkolova E, Klima M, Nencka R, Boura E. Structural analysis of the putative SARS-CoV-2 primase complex. J Struct Biol. 2020 Aug 1;211(2):107548. doi: 10.1016/j.jsb.2020.107548. Epub, 2020 Jun 11. PMID:32535228 doi:http://dx.doi.org/10.1016/j.jsb.2020.107548
↑ ^3.0 ^3.1 ^3.2 Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA, Campbell EA. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex. Cell. 2020 Jul 28. pii: S0092-8674(20)30941-7. doi: 10.1016/j.cell.2020.07.033. PMID:32783916 doi:http://dx.doi.org/10.1016/j.cell.2020.07.033
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells. 2020 May 20;9(5). pii: cells9051267. doi: 10.3390/cells9051267. PMID:32443810 doi:http://dx.doi.org/10.3390/cells9051267
↑ Krafcikova P, Silhan J, Nencka R, Boura E. Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nat Commun. 2020 Jul 24;11(1):3717. doi: 10.1038/s41467-020-17495-9. PMID:32709887 doi:http://dx.doi.org/10.1038/s41467-020-17495-9
↑ Yuen CK, Lam JY, Wong WM, Mak LF, Wang X, Chu H, Cai JP, Jin DY, To KK, Chan JF, Yuen KY, Kok KH. SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerg Microbes Infect. 2020 Dec;9(1):1418-1428. doi:, 10.1080/22221751.2020.1780953. PMID:32529952 doi:http://dx.doi.org/10.1080/22221751.2020.1780953

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Jaime Prilusky, Lea C. von Soosten, Michal Harel

[Yoshimoto-1] 1.0 ^1.1 Yoshimoto FK. The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. Protein J. 2020 Jun;39(3):198-216. doi: 10.1007/s10930-020-09901-4. PMID:32447571 doi:http://dx.doi.org/10.1007/s10930-020-09901-4

[Konkolova-2] Konkolova E, Klima M, Nencka R, Boura E. Structural analysis of the putative SARS-CoV-2 primase complex. J Struct Biol. 2020 Aug 1;211(2):107548. doi: 10.1016/j.jsb.2020.107548. Epub, 2020 Jun 11. PMID:32535228 doi:http://dx.doi.org/10.1016/j.jsb.2020.107548

[Chen-3] 3.0 ^3.1 ^3.2 Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA, Campbell EA. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex. Cell. 2020 Jul 28. pii: S0092-8674(20)30941-7. doi: 10.1016/j.cell.2020.07.033. PMID:32783916 doi:http://dx.doi.org/10.1016/j.cell.2020.07.033

[Romano-4] 4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells. 2020 May 20;9(5). pii: cells9051267. doi: 10.3390/cells9051267. PMID:32443810 doi:http://dx.doi.org/10.3390/cells9051267

[Krafcikova-5] Krafcikova P, Silhan J, Nencka R, Boura E. Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nat Commun. 2020 Jul 24;11(1):3717. doi: 10.1038/s41467-020-17495-9. PMID:32709887 doi:http://dx.doi.org/10.1038/s41467-020-17495-9

[Yuen-6] Yuen CK, Lam JY, Wong WM, Mak LF, Wang X, Chu H, Cai JP, Jin DY, To KK, Chan JF, Yuen KY, Kok KH. SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerg Microbes Infect. 2020 Dec;9(1):1418-1428. doi:, 10.1080/22221751.2020.1780953. PMID:32529952 doi:http://dx.doi.org/10.1080/22221751.2020.1780953

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-<SX viewer='molstar' load='6zsl' size='340' side='right' caption='Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution (PDB 6ZSL).' scene=''>
+<SX viewer='molstar' load='6zsl' size='340' side='right' caption='Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution (PDB 6zsl).' scene=''>
 '''Non-structural protein 13 (nsp13)/ Helicase (Hel)'''
@@ Line 16: / Line 16: @@
 Nsp13 comprises of five domains: The N-terminal Zinc binding domain (ZBD) (amino acids 1-100), the stalk domain (101-150), 1B (151-261), 1A (262-442), and the 2A domain (443-601). The last three have been shown to be responsible for nucleic acid binding and the NTPase activity, while the ZBD and 1A can directly interact with nsp12 to enhance the helicase activity of nsp13. Together they fold in a triangular shape with 1A, 1B and 2A forming the base and the stalk domain and ZBD at the apex<ref name="Romano"/>. Nsp13 might form a stable holo-RdRp complex with [[SARS-CoV-2 enzyme RdRp|nsp12]], [[SARS-CoV-2 protein NSP7|nsp7]] and [[SARS-CoV-2 protein NSP8|nsp8]] by interacting with the nsp8 extensions and the nsp12 thumb domain and may play a role in backtracking<ref name="Chen"/>.
 == See also ==