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Ebola Virus RNA-Dependent RNA Polymerase

spinqualitylabelsall models Ebola Virus RNA-Dependent RNA Polymerase Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Disease Ebola virus (EBOV) causes Ebola virus disease (EVD), a fatal hemorrhagic disease discovered in 1976. Sources of infection are mainly linked with “hunting wildlife, exposure to animal carcasses found in the forest, or contact with the putative virus reservoir, bats”. EVD pathogenesis in humans consists of three phases with symptoms normally occurring after an incubation period of 2-21 days. In the first phase, symptoms during the first few days include nonspecific fever, headache, and myalgia. This is followed by a “gastrointestinal phase” characterized by symptoms including diarrhea, vomiting, abdominal discomfort, and dehydration. The final and advanced phase of the illness consist of kidney and liver function failure, often resulting in “metabolic compromise, convulsion, shock, and death due to mucosal bleeding, bloody diarrhea, and multi-organ failure within 16 days after the first symptoms appear”. Since EBOV's discovery, there have been 20 known outbreaks restricted primarily to African countries with minor spread to neighboring countries. The most recent outbreak of Ebola occurred during a three-month span in the Democratic Republic of the Congo this year (2021), the country’s 4th in the past three years.[1] Since its start in February, there was a total of eleven confirmed cases with six recoveries and six deaths and one probable case emanating from four health zones in North Kivu.[2] There is also an ongoing outbreak in Guinea, West Africa which started in the same month as the outbreak in the DRC.[3] There is currently no vaccine for EVD, but there are currently eight vaccine candidates in human clinical trials that all target the Ebola virus glycoprotein (GP), one of the nine known proteins to be expressed by the virus’s genome. However, these vaccines are different from each other in the immune responses they elicit, the antigen delivery system, and their respective side-effect profiles. RNA Classification Ebola is part of the Filoviridae family of single-stranded negative-sense RNA viruses of approximately 19 kb. The 19 kb RNA encodes for “glycoproteins (i.e., GP, sGP, ssGP), nucleoproteins, virion proteins (i.e., VP 24, 30, 40) and the RNA-dependent RNA polymerase”. In EBOV, the RNA-dependent RNA polymerase in conjunction with NP, VP30, and VP35 form the RNP complex in viral genome transcription and replication. RdRp binds to the 3’ leader promoter and changes EBOV’s negative-sense RNA into positive-sense messenger RNA to produce Ebola proteins that produce new viral particles (virions). Function of RNA-Dependent RNA Polymerase RNA-dependent RNA polymerases (RdRp) are critical to the replication and transcription of RNA viruses. Due to this protein's importance in the viral life cycle, they are feasible targets for vaccine development. There are several antiviral drugs that have been approved that target the EBOV RdRp, including Brincidofovir (CMX-001), Lamivudine and Favipiravir (T-705). Inhibition of RdRp results in the inhibition of transcription of the viral genome, ultimately resulting in no new production of virions for the virus. Without the production of virions, the virus is no longer able to spread. Structural Features of Ebola Virus RNA-Dependent RNA Polymerase[4] EBOV has a monomeric RNA-dependent RNA polymerase and as such, shares the characteristic right hand shape of other monomeric RdRp composed of the fingertips, palm, and thumb subdomains. The predicted 3D structure described here was produced by running one Zaire Ebola virus L protein sequence (Sierra Leona, Makona-G3686.1; AIE11922) on the homology modeling program, SwissModel. [5] The fingertips subdomain is composed of residues 417-439 and 489-563, the palm subdomain is composed of residues 440-488 and 563-666, and the thumb subdomain is made up of residues 667-704. The highly conserved motifs A-F were identified in the palm subdomain of the EBOV RdRp, but motifs G and H, which are not part of the active site, were not identified. The predicted motif A is composed of a β-strand followed by a loop 10 amino acids long. It is in motif A that you find the highly conserved residue 624 that is one of two catalytic aspartic acid residues (the other being residue 734 in motif C). Motif B is composed of a loop followed by a long α-helix. Residues 564-568 found in motif B may be involved in interacting with the incoming nucleotide and the template RNA. Motif C possesses the structure β-strand-loop-β-strand and has an aspartate residue that matches the conserved and catalytic Asp593 found in other RdRp in the Mononegavirales order. The aspartate residues in this model interact with metal ions, coordinating their position, and the residues are also involved in completing the nucleotidyl transfer reaction. Motif D is formed by an α-helix and a long loop. Motif D contains two conserved amino acids of importance. Lysine 639 and glutamic acid 642 are both conserved in the Mononegavirales order, and depronate the pyrophosphate leaving group and interact with the incoming nucleotide, respectively. Additionally, motif D serves as a structural scaffold for the palm subdomain as it is composed predominantly of hydrophobic residues. Motif E has the characteristic β-hairpin structure and is in charge of positioning the 3' OH end of the primer during transcription. Motif F is composed of several basic residues and is likely involved in RNA binding. There are a number of conserved residues in EBOV RdRp that are involved in template-primer binding (residues 545, 547, 553, 627, 705-706, 708-709, 780, 783, 795-796, 801, 809, 813.