5saa - Revision history

OCA at 09:59, 22 May 2024

OCA — Wed, 22 May 2024 09:59:19 GMT

←Older revision		Revision as of 09:59, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5saa]] 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=5SAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5saa]] 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=5SAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SAA 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=ZQD:3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole'>ZQD</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]] 2.239Å</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=ZQD:3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole'>ZQD</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=5saa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5saa OCA], [https://pdbe.org/5saa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5saa RCSB], [https://www.ebi.ac.uk/pdbsum/5saa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5saa 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=5saa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5saa OCA], [https://pdbe.org/5saa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5saa RCSB], [https://www.ebi.ac.uk/pdbsum/5saa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5saa ProSAT]</span></td></tr>
	</table>		</table>
Line 13:		Line 14:
	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 ~~Apr 28~~:~~gkad314~~. doi: 10.1093/nar/gkad314. PMID:37115000<ref>PMID:37115000</ref>	+	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 5saa" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5saa" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridylate-specific endoribonuclease\|Uridylate-specific endoribonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:00, 10 May 2023

OCA — Wed, 10 May 2023 07:00:25 GMT

←Older revision		Revision as of 07:00, 10 May 2023
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284==		==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284==
-	<StructureSection load='5saa' size='340' side='right'caption='[[5saa]]' scene=''>	+	<StructureSection load='5saa' size='340' side='right'caption='[[5saa]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5saa]] 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=5SAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SAA FirstGlance]. <br>
-	</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=5saa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5saa OCA], [https://pdbe.org/5saa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5saa RCSB], [https://www.ebi.ac.uk/pdbsum/5saa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5saa ProSAT]</span></td></tr>	+	</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=ZQD:3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole'>ZQD</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=5saa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5saa OCA], [https://pdbe.org/5saa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5saa RCSB], [https://www.ebi.ac.uk/pdbsum/5saa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5saa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/R1AB_SARS2 R1AB_SARS2] Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.[UniProtKB:P0C6X7] Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.[UniProtKB:P0C6X7] May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.[UniProtKB:P0C6X7] Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.[UniProtKB:P0C6X7] Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.[UniProtKB:P0C6X7] Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN] (PubMed:32198291). Also able to bind an ADP-ribose-1''-phosphate (ADRP).[UniProtKB:P0C6X7]<ref>PMID:32198291</ref> Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] May participate in viral replication by acting as a ssRNA-binding protein.[UniProtKB:P0C6X7] Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.[UniProtKB:P0C6X7] Responsible for replication and transcription of the viral RNA genome.[UniProtKB:P0C6X7] Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium.[UniProtKB:P0C6X7] Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Acts as a proofreading exoribonuclease for RNA replication, thereby lowering The sensitivity of the virus to RNA mutagens.[UniProtKB:P0C6X7] Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.[UniProtKB:P0C6X7] Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system.[UniProtKB:P0C6X7]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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 Apr 28:gkad314. 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>
		+	</div>
		+	<div class="pdbe-citations 5saa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Aimon A]]		[[Category: Aimon A]]
	[[Category: Brandao-Neto J]]		[[Category: Brandao-Neto J]]

OCA at 12:08, 9 June 2021

OCA — Wed, 09 Jun 2021 12:08:25 GMT

←Older revision		Revision as of 12:08, 9 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5saa ~~is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284==
-		+	<StructureSection load='5saa' size='340' side='right'caption='[[5saa]]' scene=''>
-	~~Authors~~: ~~Godoy, A~~.S.~~, Douangamath, A~~.~~, Nakamura, A~~.M.~~, Dias, A~~.~~, Krojer, T~~.~~, Noske, G~~.D., ~~Gawiljuk, V~~.O.~~, Fernandes, R.S~~., ~~Fairhead, M~~., ~~Powell, A~~.~~, Dunnet, L~~.~~, Aimon, A~~., ~~Fearon, D~~.~~, Brandao-Neto, J~~.~~, Skyner, R~~., ~~von Delft, F~~.~~, Oliva, G~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SAA FirstGlance]. <br>
-	~~Description: PanDDA analysis group deposition --Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284~~	+	</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=5saa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5saa OCA], [https://pdbe.org/5saa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5saa RCSB], [https://www.ebi.ac.uk/pdbsum/5saa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5saa ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Aimon, A]]	+	__TOC__
-	[[Category: ~~Noske, G.D~~]]	+	</StructureSection>
-	[[Category: ~~Brandao-Neto, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Powell,~~ A]]	+	[[Category: Aimon A]]
-	[[Category: ~~Fernandes, R.S~~]]	+	[[Category: Brandao-Neto J]]
-	[[Category: ~~Godoy, A.S~~]]	+	[[Category: Dias A]]
-	[[Category: Fearon, D]]	+	[[Category: Douangamath A]]
-	[[Category: ~~Oliva, G~~]]	+	[[Category: Dunnet L]]
-	[[Category: ~~Fairhead, M~~]]	+	[[Category: Fairhead M]]
-	[[Category: ~~Gawiljuk, V.O~~]]	+	[[Category: Fearon D]]
-	[[Category: ~~Von Delft, F~~]]	+	[[Category: Fernandes RS]]
-	[[Category: Nakamura~~, A.M~~]]	+	[[Category: Gawiljuk VO]]
-	[[Category: ~~Dunnet, L~~]]	+	[[Category: Godoy AS]]
-	[[Category: ~~Skyner, R~~]]	+	[[Category: Krojer T]]
-	[[Category: ~~Douangamath,~~ A]]	+	[[Category: Nakamura AM]]
-	[[Category: ~~Krojer, T~~]]	+	[[Category: Noske GD]]
-	[[Category: ~~Dias, A~~]]	+	[[Category: Oliva G]]
		+	[[Category: Powell A]]
		+	[[Category: Skyner R]]
		+	[[Category: Von Delft F]]

OCA: Protected "5saa" [edit=sysop:move=sysop]

OCA — Wed, 26 May 2021 07:44:45 GMT

Protected "5saa" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:44, 26 May 2021

OCA: New page: '''Unreleased structure''' The entry 5saa is ON HOLD Authors: Godoy, A.S., Douangamath, A., Nakamura, A.M., Dias, A., Krojer, T., Noske, G.D., Gawiljuk, V.O., Fernandes, R.S., Fairhead,...

OCA — Wed, 26 May 2021 07:44:44 GMT

New page: '''Unreleased structure''' The entry 5saa is ON HOLD Authors: Godoy, A.S., Douangamath, A., Nakamura, A.M., Dias, A., Krojer, T., Noske, G.D., Gawiljuk, V.O., Fernandes, R.S., Fairhead,...

New page

'''Unreleased structure'''

The entry 5saa is ON HOLD

Authors: Godoy, A.S., Douangamath, A., Nakamura, A.M., Dias, A., Krojer, T., Noske, G.D., Gawiljuk, V.O., Fernandes, R.S., Fairhead, M., Powell, A., Dunnet, L., Aimon, A., Fearon, D., Brandao-Neto, J., Skyner, R., von Delft, F., Oliva, G.

Description: PanDDA analysis group deposition --Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284
[[Category: Unreleased Structures]]
[[Category: Aimon, A]]
[[Category: Noske, G.D]]
[[Category: Brandao-Neto, J]]
[[Category: Powell, A]]
[[Category: Fernandes, R.S]]
[[Category: Godoy, A.S]]
[[Category: Fearon, D]]
[[Category: Oliva, G]]
[[Category: Fairhead, M]]
[[Category: Gawiljuk, V.O]]
[[Category: Von Delft, F]]
[[Category: Nakamura, A.M]]
[[Category: Dunnet, L]]
[[Category: Skyner, R]]
[[Category: Douangamath, A]]
[[Category: Krojer, T]]
[[Category: Dias, A]]