scholarly journals NMPylation and de-NMPylation of SARS-CoV-2 Nsp9 by the NiRAN domain

2021 ◽  
Author(s):  
Bing Wang ◽  
Dmitri Svetlov ◽  
Irina Artsimovitch

Nsp12, the catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), contains two active sites that catalyze nucleotidyl-monophosphate (NMP) transfer (NMPylation). RNA synthesis is mediated by the RdRp active site that is conserved among all RNA viruses and has been a focus of mechanistic studies and drug discovery. The second active site resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain. Both catalytic reactions are essential for viral replication, but the mechanism and targets of NiRAN are poorly characterized. One recent study showed that NiRAN transfers NMP to the first residue of RNA-binding protein Nsp9. Another study reported a structure of SARS-CoV-2 replicase with an extended Nsp9 in the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 Nsp12 efficiently and reversibly NMPylates the native but not the extended Nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas a substitution of a catalytic RdRp Asp residue does not. NMPylation is inhibited by nucleotide analogs, pyrophosphate, and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We hypothesize that Nsp9 remodels both active sites of Nsp12 to support initiation of RNA synthesis by RdRp and subsequent capping of the product RNA by the NiRAN domain.

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1738
Author(s):  
Alesia A. Levanova ◽  
Eeva J. Vainio ◽  
Jarkko Hantula ◽  
Minna M. Poranen

Heterobasidion RNA virus 6 (HetRV6) is a double-stranded (ds)RNA mycovirus and a member of the recently established genus Orthocurvulavirus within the family Orthocurvulaviridae. The purpose of the study was to determine the biochemical requirements for RNA synthesis catalyzed by HetRV6 RNA-dependent RNA polymerase (RdRp). HetRV6 RdRp was expressed in Escherichia coli and isolated to near homogeneity using liquid chromatography. The enzyme activities were studied in vitro using radiolabeled UTP. The HetRV6 RdRp was able to initiate RNA synthesis in a primer-independent manner using both virus-related and heterologous single-stranded (ss)RNA templates, with a polymerization rate of about 46 nt/min under optimal NTP concentration and temperature. NTPs with 2′-fluoro modifications were also accepted as substrates in the HetRV6 RdRp-catalyzed RNA polymerization reaction. HetRV6 RdRp transcribed viral RNA genome via semi-conservative mechanism. Furthermore, the enzyme demonstrated terminal nucleotidyl transferase (TNTase) activity. Presence of Mn2+ was required for the HetRV6 RdRp catalyzed enzymatic activities. In summary, our study shows that HetRV6 RdRp is an active replicase in vitro that can be potentially used in biotechnological applications, molecular biology, and biomedicine.


2019 ◽  
Vol 21 (3) ◽  
pp. 704-711 ◽  
Author(s):  
Fan Yang ◽  
Minjian Wang ◽  
Wei Liu ◽  
Bin Yang ◽  
Ying Wang ◽  
...  

Noble-metal-free catalytic hydrogenation of nitroarenes is achieved through the rational design of atomically dispersed Ni sites on N-doped porous carbon. The outstanding activity of the catalyst originates from the atomic dispersion of Ni active sites with a high Ni–N3 content.


2020 ◽  
Author(s):  
Jack PK Bravo ◽  
Tyler L Dangerfield ◽  
David W Taylor ◽  
Kenneth A Johnson

Remdesivir is a nucleoside analog approved by the FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryoEM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of three copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of three bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs.


Author(s):  
Akira Oda ◽  
Koshiro Aono ◽  
Naoya Murata ◽  
Kazumasa Murata ◽  
Masazumi Yasumoto ◽  
...  

Iron-containing zeolite possesses an active site capable of low-temperature partial oxidation of methane using hydrogen peroxide as an environmentally benign oxidant. However, only a trace number of active sites has...


2003 ◽  
Vol 77 (16) ◽  
pp. 9020-9028 ◽  
Author(s):  
Vincent J.-P. Lévêque ◽  
Robert B. Johnson ◽  
Stephen Parsons ◽  
Jianxin Ren ◽  
Congping Xie ◽  
...  

ABSTRACT The NS5B RNA-dependent RNA polymerase encoded by the hepatitis C virus (HCV) is a key component of the viral replicase. Reported here is the three-dimensional structure of HCV NS5B polymerase, with the highlight on its C-terminal folding, determined by X-ray crystallography at 2.1-Å resolution. Structural analysis revealed that a stretch of C-terminal residues of HCV NS5B inserted into the putative RNA binding cleft, where they formed a hydrophobic pocket and interacted with several important structural elements. This region was found to be conserved and unique to the RNA polymerases encoded by HCV and related viruses. Through biochemical analyses, we confirmed that this region interfered with the binding of HCV NS5B to RNA. Deletion of this fragment from HCV NS5B enhanced the RNA synthesis rate up to ∼50-fold. These results provide not only direct experimental insights into the role of the C-terminal tail of HCV NS5B polymerase but also a working model for the RNA synthesis mechanism employed by HCV and related viruses.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. SCI-7-SCI-7 ◽  
Author(s):  
Egon Persson

Abstract The formation of a complex between factor VIIa (FVIIa) and tissue factor (TF) triggers the blood coagulation cascade in response to a vascular injury. TF has the dual biological function of localizing FVIIa to the site of injury and converting the latent enzyme into an efficient catalyst of factor VII, IX, and X activation. The hemostatic effect of recombinant FVIIa in hemophilia patients, where FVIIa is present at supraphysiological concentrations, is however largely mediated by factor X activation on the surface of activated platelets to which FVIIa binds with relatively low affinity. In this setting, it would be pharmacodynamically advantageous to dispose of FVIIa variants with enhanced intrinsic activity. Moreover, such variants might shed light on how TF induces maturation of the active conformation of FVIIa. Intuitively, more active variants of FVIIa could be designed by exploiting structural differences between FVIIa before and after binding to TF. To get the most out of this approach, the structures of free, uninhibited FVIIa and TF-bound FVIIa should be available for comparison. This is because an active-site inhibitor shifts FVIIa into an active conformation and locks it there, and conformational transitions in the same direction normally induced by TF binding may already have occurred upon inhibitor incorporation or be obscured or even prevented. Unfortunately, crystallization attempts with FVIIa without an active-site inhibitor have not been fruitful, neither with nor without TF. Nevertheless, a few structural clues have been identified, one of which was an attempted mimick by mutagenesis that led to the discovery of the modestly superactive L305V-FVIIa (1). The design and generation of more active FVIIa variants by exploiting sequence differences between FVIIa and homologous enzymes, whose active sites expedite catalytic events at a higher rate, has been more successful. The most striking outcome of this particular endeavour is V158D/E296V/M298Q-FVIIa (FVIIaDVQ) (2, 3).In FVIIaDVQ, three amino acid residues in FVIIa have been replaced by those occupying the corresponding positions in thrombin and factor IXa. Interestingly, the conformational changes induced by the three replacements have been shown to be a subset of those brought about by TF. It is fair to state that FVIIaDVQ is a conformational intermediate between free and TF-bound FVIIa and that the molecule strives to imitate the latter. FVIIaDVQ is dramatically more efficient in cleaving substrates in the absence of TF compared with FVIIa, whereas the specific activities of the two forms of FVIIa bound to TF are comparable. This has also been demonstrated on cellular representations of the two conditions, namely platelets and LPS-stimulated monocytes, respectively. The high activity of FVIIaDVQ has also manifested itself as an increased potency and more rapid effect in murine bleeding models compared with FVIIa and in vitro normalization of human hemophilic blood clotting. An indication of an improved efficacy rate of FVIIaDVQ compared with the efficient drug recombinant FVIIa was observed in a clinical trial (4). 1. Persson E, Bak H., Olsen O.H. Substitution of valine for leucine 305 in factor VIIa increases the intrinsic enzymatic activity. J Biol Chem.2001;276(31):29195-29199. 2. Persson E, Kjalke M., Olsen O.H. Rational design of coagulation factor VIIa variants with substantially increased intrinsic activity. Proc Natl Acad Sci USA.2001;98(24):13583-13588. 3. Persson E., Olsen O.H., Bjørn S.E., Ezban M. Vatreptacog alfa from conception to clinical proof of concept. Semin Thromb Hemost. 2012;38(3):274-281. 4. De Paula E.V., Kavakli K., Mahlangu J., et al. Recombinant factor VIIa analog (vatreptacog alfa [activated]) for treatment of joint bleeds in hemophilia patients with inhibitors: a randomized controlled trial. J Thromb Haemost. 2012;10(1):81-89. Disclosures: No relevant conflicts of interest to declare.


2019 ◽  
Vol 294 (45) ◽  
pp. 16897-16907 ◽  
Author(s):  
Alyson K. Boehr ◽  
Jamie J. Arnold ◽  
Hyung S. Oh ◽  
Craig E. Cameron ◽  
David D. Boehr

2010 ◽  
Vol 427 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Charlotte A. Dodson ◽  
Magda Kosmopoulou ◽  
Mark W. Richards ◽  
Butrus Atrash ◽  
Vassilios Bavetsias ◽  
...  

The production of selective protein kinase inhibitors is often frustrated by the similarity of the enzyme active sites. For this reason, it is challenging to design inhibitors that discriminate between the three Aurora kinases, which are important targets in cancer drug discovery. We have used a triple-point mutant of Aurora-A (AurAx3) which mimics the active site of Aurora-B to investigate the structural basis of MLN8054 selectivity. The bias toward Aurora-A inhibition by MLN8054 is fully recapitulated by AurAx3in vitro. X-ray crystal structures of the complex suggest that the basis for the discrimination is electrostatic repulsion due to the T217E substitution, which we have confirmed using a single-point mutant. The activation loop of Aurora-A in the AurAx3–MLN8054 complex exhibits an unusual conformation in which Asp274 and Phe275 side chains point into the interior of the protein. There is to our knowledge no documented precedent for this conformation, which we have termed DFG-up. The sequence requirements of the DFG-up conformation suggest that it might be accessible to only a fraction of kinases. MLN8054 thus circumvents the problem of highly homologous active sites. Binding of MLN8054 to Aurora-A switches the character of a pocket within the active site from polar to a hydrophobic pocket, similar to what is observed in the structure of Aurora-A bound to a compound that induces DFG-out. We propose that targeting this pocket may be a productive route in the design of selective kinase inhibitors and describe the structural basis for the rational design of these compounds.


2000 ◽  
Vol 74 (22) ◽  
pp. 10312-10322 ◽  
Author(s):  
Min-Ju Kim ◽  
Weidong Zhong ◽  
Zhi Hong ◽  
C. Cheng Kao

ABSTRACT The recombinant RNA-dependent RNA polymerase of the bovine viral diarrhea virus specifically requires a cytidylate at the 3′ end for the de novo initiation of RNA synthesis (C. C. Kao, A. M. Del Vecchio, and W. Zhong, Virology 253:1–7, 1999). Using RNAs containing nucleotide analogs, we found that the N3 and C4-amino group at the initiation cytidine were required for RNA synthesis. However, the ribose C2′-hydroxyl of the initiating cytidylate can accept several modifications and retain the ability to direct synthesis. The only unacceptable modification is a protonated C2′-amino group. Quite strikingly, the recognition of the functional groups for the initiation cytidylate and other template nucleotides are different. For example, a C5-methyl group in cytidine can direct RNA synthesis at all template positions except at the initiation cytidylate and C2′-amino modifications are tolerated better after the +11 position. When a 4-thiouracil (4sU) base analog that allows only imperfect base pairing with the nascent RNA is placed at different positions in the template, the efficiency of synthesis is correlated with the calculated stability of the template-nascent RNA duplex adjacent to the position of the 4sU. These results define the requirements for the specific interactions required for the initiation of RNA synthesis and will be compared to the mechanisms of initiation by other RNA-dependent and DNA-dependent RNA polymerases.


2021 ◽  
Author(s):  
James Chen ◽  
Qi Wang ◽  
Brandon Malone ◽  
Eliza Llewellyn ◽  
Yakov Pechersky ◽  
...  

The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex, or RTC) associated with two copies of nsp13 (nsp132-RTC). One copy of nsp13 interacts with the template RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backwards on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here, we use cryo-electron microscopy and molecular dynamics simulations to analyze the nsp132-RTC, revealing four distinct conformational states of the helicases. The results suggest a mechanism for the nsp132-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.


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