5sa5: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5sa5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SA5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SA5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[5sa5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SA5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SA5 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZQA:4-ethyl-2-(1H-imidazol-5-yl)-1,3-thiazole'>ZQA</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZQA:4-ethyl-2-(1H-imidazol-5-yl)-1,3-thiazole'>ZQA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5sa5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sa5 OCA], [https://pdbe.org/5sa5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sa5 RCSB], [https://www.ebi.ac.uk/pdbsum/5sa5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sa5 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5sa5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sa5 OCA], [https://pdbe.org/5sa5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sa5 RCSB], [https://www.ebi.ac.uk/pdbsum/5sa5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sa5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors. | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors. | ||
Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.,Godoy AS, Nakamura AM, Douangamath A, Song Y, Noske GD, Gawriljuk VO, Fernandes RS, Pereira HDM, Oliveira KIZ, Fearon D, Dias A, Krojer T, Fairhead M, Powell A, Dunnet L, Brandao-Neto J, Skyner R, Chalk R, Bajusz D, Bege M, Borbas A, Keseru GM, von Delft F, Oliva G Nucleic Acids Res. 2023 | Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.,Godoy AS, Nakamura AM, Douangamath A, Song Y, Noske GD, Gawriljuk VO, Fernandes RS, Pereira HDM, Oliveira KIZ, Fearon D, Dias A, Krojer T, Fairhead M, Powell A, Dunnet L, Brandao-Neto J, Skyner R, Chalk R, Bajusz D, Bege M, Borbas A, Keseru GM, von Delft F, Oliva G Nucleic Acids Res. 2023 Jun 9;51(10):5255-5270. doi: 10.1093/nar/gkad314. PMID:37115000<ref>PMID:37115000</ref> | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 5sa5" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5sa5" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Uridylate-specific endoribonuclease|Uridylate-specific endoribonuclease]] | |||
== References == | == References == | ||
<references/> | <references/> | ||