7eww - Revision history

OCA at 17:05, 29 November 2023

OCA — Wed, 29 Nov 2023 17:05:39 GMT

←Older revision		Revision as of 17:05, 29 November 2023
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	<StructureSection load='7eww' size='340' side='right'caption='[[7eww]], [[Resolution\|resolution]] 2.34Å' scene=''>		<StructureSection load='7eww' size='340' side='right'caption='[[7eww]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7eww]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EWW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eww]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ebinur_lake_virus Ebinur lake virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EWW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.34Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=7eww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eww OCA], [https://pdbe.org/7eww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eww RCSB], [https://www.ebi.ac.uk/pdbsum/7eww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eww 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=7eww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eww OCA], [https://pdbe.org/7eww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eww RCSB], [https://www.ebi.ac.uk/pdbsum/7eww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eww ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A059WLS9_9VIRU A0A059WLS9_9VIRU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ebinur lake virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: RNA-directed RNA polymerase]]~~	+	[[Category: Gong P]]
-	[[Category: Gong, P]]	+	[[Category: Hu Z]]
-	[[Category: Hu, Z]]	+	[[Category: Kuang W]]
-	[[Category: Kuang, W]]	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:25, 2 March 2022

OCA — Wed, 02 Mar 2022 07:25:54 GMT

←Older revision		Revision as of 07:25, 2 March 2022
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	==Crystal structure of Ebinur Lake virus cap snatching endonuclease (N52A mutant)==		==Crystal structure of Ebinur Lake virus cap snatching endonuclease (N52A mutant)==
-	<StructureSection load='7eww' size='340' side='right'caption='[[7eww]]' scene=''>	+	<StructureSection load='7eww' size='340' side='right'caption='[[7eww]], [[Resolution\|resolution]] 2.34Å' 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=7EWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EWW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eww]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EWW 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=7eww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eww OCA], [https://pdbe.org/7eww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eww RCSB], [https://www.ebi.ac.uk/pdbsum/7eww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eww 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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=7eww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eww OCA], [https://pdbe.org/7eww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eww RCSB], [https://www.ebi.ac.uk/pdbsum/7eww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eww ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cap-snatching endonuclease (EN) of segmented negative-strand RNA viruses (sNSVs) produces short capped primers for viral transcription by cleaving the host mRNAs. EN requires divalent metals as cofactors for nucleic acid substrates cleavage, however, the detailed mechanism of metal ion-dependent catalysis of ENs remains obscure. In this work, we reported the EN crystal structure of the Ebinur Lake virus (EBIV), an emerging mosquito-borne orthobunyavirus, and investigated its enzymatic properties and metal ion-based catalytic mechanism. In vitro biochemical data showed that EBIV EN is a specific RNA nuclease and prefers to cleave unstructured uridine-rich ssRNA. Structural comparison indicated that the overall structural architecture of EBIV EN is similar to that of other sNSV ENs, while the detailed active site configuration including the binding state of metal ions and the conformation of the LA/LB loop pair is different. Base on sequence conservation analysis, nine active site mutants were constructed, and seven crystal structures of them were determined. Mutations of active site residues associated with the two metal ions (Mn1 and Mn2) coordination abolished EN activity. Crystallographic analyses further revealed that none of these mutants bound two metal ions simultaneously in the active site. Importantly, we found that the perturbation of Mn1-coordination (metal site 1), resulted in the enhancement or elimination of Mn2-coordination (metal site 2). Taken together, our data provide structural evidence to support the two-metal-ion catalytic mechanism of EBIV EN and the correlation of metal binding at the two binding sites, which may be commonly shared by bunyaviruses or other sNSVs. IMPORTANCE The viral endonucleases (ENs) encoded by bunyaviruses and orthomyxoviruses play an essential role in initiating transcription by "snatching" capped primers from the host mRNAs. These ENs are metal-ion-dependent nucleases, however, the details of their catalytic mechanism remain elusive. Here, we reported high-resolution crystal structures of the wild-type and mutant ENs of a novel bunyavirus, the Ebinur Lake virus (EBIV), and revealed the structure and function relationship of EN. The EBIV EN exhibited differences in the details of active site structure compared to its homologues. Our data provided structural evidence to support a two-metal-ion catalytic mechanism of EBIV EN, and found the correlation of metal binding at both binding sites, which might reflect the dynamic structural properties that correlate to EN catalytic function. Taken together, our results revealed the structural characteristics of EBIV EN and made important implications for understanding the catalytic mechanism of cap-snatching ENs.
		+
		+	Insights into two-metal-ion catalytic mechanism of cap-snatching endonuclease of Ebinur Lake virus in Bunyavirales.,Kuang W, Zhang H, Cai Y, Zhang G, Deng F, Li H, Hu Z, Guo Y, Wang M, Zhou Y, Gong P J Virol. 2022 Jan 19:jvi0208521. doi: 10.1128/jvi.02085-21. PMID:35044209<ref>PMID:35044209</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7eww" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gong P]]	+	[[Category: RNA-directed RNA polymerase]]
-	[[Category: Hu Z]]	+	[[Category: Gong, P]]
-	[[Category: Kuang W]]	+	[[Category: Hu, Z]]
		+	[[Category: Kuang, W]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase]]

OCA at 07:00, 27 January 2022

OCA — Thu, 27 Jan 2022 07:00:23 GMT

←Older revision		Revision as of 07:00, 27 January 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7eww is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Ebinur Lake virus cap snatching endonuclease (N52A mutant)==
-		+	<StructureSection load='7eww' size='340' side='right'caption='[[7eww]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EWW FirstGlance]. <br>
-	~~Description~~:	+	</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=7eww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eww OCA], [https://pdbe.org/7eww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eww RCSB], [https://www.ebi.ac.uk/pdbsum/7eww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eww ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gong P]]
		+	[[Category: Hu Z]]
		+	[[Category: Kuang W]]

OCA at 10:57, 9 June 2021

OCA — Wed, 09 Jun 2021 10:57:29 GMT

←Older revision		Revision as of 10:57, 9 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7eww is ON HOLD	+	The entry 7eww is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7eww" [edit=sysop:move=sysop]

OCA — Wed, 02 Jun 2021 13:25:00 GMT

Protected "7eww" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:25, 2 June 2021

OCA: New page: '''Unreleased structure''' The entry 7eww is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Jun 2021 13:24:59 GMT

New page: '''Unreleased structure''' The entry 7eww is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7eww is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]