5ecw - Revision history

OCA at 06:21, 5 July 2023

OCA — Wed, 05 Jul 2023 06:21:36 GMT

←Older revision		Revision as of 06:21, 5 July 2023
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	==Structure of the Shigella flexneri VapC mutant D7A==		==Structure of the Shigella flexneri VapC mutant D7A==
-	<StructureSection load='5ecw' size='340' side='right' caption='[[5ecw]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='5ecw' size='340' side='right'caption='[[5ecw]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ecw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ECW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ecw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ECW FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5ecd\|5ecd]]</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]] 1.94Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">vapC, mvpA, stborf2, CP0245 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])~~</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=5ecw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecw OCA], [https://pdbe.org/5ecw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ecw RCSB], [https://www.ebi.ac.uk/pdbsum/5ecw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ecw ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ecw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecw OCA], [~~http~~://pdbe.org/5ecw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ecw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ecw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ecw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VAPC_SHIFL VAPC_SHIFL]] Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref>	+	[https://www.uniprot.org/uniprot/VAPC_SHIFL VAPC_SHIFL] Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ecw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ecw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Shigella paradysenteriae weldin 1927~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Brodersen, D E~~]]	+	[[Category: Shigella flexneri]]
-	[[Category: ~~Dedic, E~~]]	+	[[Category: Brodersen DE]]
-	[[Category: ~~Xu, K~~]]	+	[[Category: Dedic E]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Xu K]]
-	~~[[Category: Pin-domain]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 08:04, 17 January 2018

OCA — Wed, 17 Jan 2018 08:04:01 GMT

←Older revision		Revision as of 08:04, 17 January 2018
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	<StructureSection load='5ecw' size='340' side='right' caption='[[5ecw]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='5ecw' size='340' side='right' caption='[[5ecw]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ecw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ECW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ecw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ECW FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ecd\|5ecd]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ecd\|5ecd]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ecw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecw OCA], [http://pdbe.org/5ecw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ecw RCSB], [http://www.ebi.ac.uk/pdbsum/5ecw PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC, mvpA, stborf2, CP0245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ecw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecw OCA], [http://pdbe.org/5ecw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ecw RCSB], [http://www.ebi.ac.uk/pdbsum/5ecw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ecw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Shigella paradysenteriae weldin 1927]]
	[[Category: Brodersen, D E]]		[[Category: Brodersen, D E]]
	[[Category: Dedic, E]]		[[Category: Dedic, E]]

OCA at 02:42, 21 February 2016

OCA — Sun, 21 Feb 2016 02:42:35 GMT

←Older revision		Revision as of 02:42, 21 February 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5ecw is ~~ON HOLD~~	+	==Structure of the Shigella flexneri VapC mutant D7A==
		+	<StructureSection load='5ecw' size='340' side='right' caption='[[5ecw]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ecw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ECW FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ecd\|5ecd]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ecw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecw OCA], [http://pdbe.org/5ecw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ecw RCSB], [http://www.ebi.ac.uk/pdbsum/5ecw PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VAPC_SHIFL VAPC_SHIFL]] Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg2+ -dependent ribonuclease and has been shown to target initiator tRNAfMet in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC appears as a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of a target nucleotide. This article is protected by copyright. All rights reserved.

-	~~Authors: Xu~~, K., Dedic, E., Brodersen~~, D~~.E.	+	Structural analysis on the active site architecture of the VapC toxin from Shigella flexneri.,Xu K, Dedic E, Brodersen DE Proteins. 2016 Feb 2. doi: 10.1002/prot.25002. PMID:26833558<ref>PMID:26833558</ref>

-	~~Description: Structure~~ of the ~~Shigella flexneri VapC mutant D7A~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Brodersen, D.E]]	+	<div class="pdbe-citations 5ecw" style="background-color:#fffaf0;"></div>
-	~~[[Category: Xu, K~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Brodersen, D E]]
	[[Category: Dedic, E]]		[[Category: Dedic, E]]
		+	[[Category: Xu, K]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pin-domain]]
		+	[[Category: Toxin]]

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

OCA — Tue, 01 Dec 2015 02:39:39 GMT

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

←Older revision

Revision as of 02:39, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5ecw is ON HOLD Authors: Xu, K., Dedic, E., Brodersen, D.E. Description: Structure of the Shigella flexneri VapC mutant D7A [[Category: Unreleased ...

OCA — Tue, 01 Dec 2015 02:39:37 GMT

New page: '''Unreleased structure''' The entry 5ecw is ON HOLD Authors: Xu, K., Dedic, E., Brodersen, D.E. Description: Structure of the Shigella flexneri VapC mutant D7A [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5ecw is ON HOLD

Authors: Xu, K., Dedic, E., Brodersen, D.E.

Description: Structure of the Shigella flexneri VapC mutant D7A
[[Category: Unreleased Structures]]
[[Category: Brodersen, D.E]]
[[Category: Xu, K]]
[[Category: Dedic, E]]