5wz4 - Revision history

OCA at 06:08, 2 March 2023

OCA — Thu, 02 Mar 2023 06:08:15 GMT

←Older revision		Revision as of 06:08, 2 March 2023
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	==Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin==		==Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin==
-	<StructureSection load='5wz4' size='340' side='right' caption='[[5wz4]], [[Resolution\|resolution]] 1.77Å' scene=''>	+	<StructureSection load='5wz4' size='340' side='right'caption='[[5wz4]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycto Mycto~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wzf\|5wzf]]</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [https://pdbe.org/5wz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [https://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC20, Rv2549c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])~~</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [~~http~~://pdbe.org/5wz4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~VPC20_MYCTU VPC20_MYCTU]~~] Toxic component of a ~~type II~~ toxin-antitoxin (TA) ~~system (PubMed:19016878, PubMed:24225902)~~. An endoribonuclease that cleaves ~~both E.coli and M.smegmatis~~ 23S rRNA ~~between G2661 and A2662~~ in the sarcin-ricin loop (SRL~~, E.coli 23S rRNA numbering~~). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA ~~in E.coli, nor on a shortened artificial substrate (PubMed:24225902). Upon expression in E.coli inhibits cell growth, colony formation and translation~~. Its toxic effect is neutralized by coexpression~~, or subsequent expression (tested over 2 hours)~~ with cognate antitoxin VapB20 ~~(PubMed:19016878, PubMed:24225902)~~.[HAMAP-Rule:MF_00265]~~<ref>PMID:19016878</ref> <ref>PMID:24225902</ref>~~	+	[https://www.uniprot.org/uniprot/VPC20_MYCTO VPC20_MYCTO] Toxic component of a toxin-antitoxin (TA) module. An endoribonuclease that cleaves 23S rRNA in the sarcin-ricin loop (SRL). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB20.[UniProtKB:P95004][HAMAP-Rule:MF_00265]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5wz4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wz4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycto~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Deep, A~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: ~~Thakur, K G~~]]	+	[[Category: Deep A]]
-	[[Category: ~~Homodimer]]~~	+	[[Category: Thakur KG]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pin-domain]]~~	+
-	~~[[Category: Sarcin-ricin loop cleaving toxin]]~~	+
-	~~[[Category: Toxin-antitoxin system]]~~	+
-	~~[[Category: Vapc toxin~~]]	+

OCA at 14:09, 11 April 2018

OCA — Wed, 11 Apr 2018 14:09:44 GMT

←Older revision		Revision as of 14:09, 11 April 2018
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	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wzf\|5wzf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wzf\|5wzf]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC20, ~~MT2626.1~~ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC20, Rv2549c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [http://pdbe.org/5wz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [http://pdbe.org/5wz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~VPC20_MYCTO VPC20_MYCTO~~]] Toxic component of a toxin-antitoxin (TA) ~~module~~. An endoribonuclease that cleaves 23S rRNA in the sarcin-ricin loop (SRL). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB20.~~[UniProtKB:P95004]~~[HAMAP-Rule:MF_00265]	+	[[http://www.uniprot.org/uniprot/VPC20_MYCTU VPC20_MYCTU]] Toxic component of a type II toxin-antitoxin (TA) system (PubMed:19016878, PubMed:24225902). An endoribonuclease that cleaves both E.coli and M.smegmatis 23S rRNA between G2661 and A2662 in the sarcin-ricin loop (SRL, E.coli 23S rRNA numbering). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA in E.coli, nor on a shortened artificial substrate (PubMed:24225902). Upon expression in E.coli inhibits cell growth, colony formation and translation. Its toxic effect is neutralized by coexpression, or subsequent expression (tested over 2 hours) with cognate antitoxin VapB20 (PubMed:19016878, PubMed:24225902).[HAMAP-Rule:MF_00265]<ref>PMID:19016878</ref> <ref>PMID:24225902</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:35, 13 December 2017

OCA — Wed, 13 Dec 2017 07:35:53 GMT

←Older revision		Revision as of 07:35, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5wz4' size='340' side='right' caption='[[5wz4]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='5wz4' size='340' side='right' caption='[[5wz4]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycto Mycto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wzf\|5wzf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wzf\|5wzf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC20, MT2626.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [http://pdbe.org/5wz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [http://pdbe.org/5wz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mycto]]
	[[Category: Deep, A]]		[[Category: Deep, A]]
	[[Category: Thakur, K G]]		[[Category: Thakur, K G]]

OCA at 07:04, 25 October 2017

OCA — Wed, 25 Oct 2017 07:04:17 GMT

←Older revision		Revision as of 07:04, 25 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wz4 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin==
		+	<StructureSection load='5wz4' size='340' side='right' caption='[[5wz4]], [[Resolution\|resolution]] 1.77Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wzf\|5wzf]]</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [http://pdbe.org/5wz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VPC20_MYCTO VPC20_MYCTO]] Toxic component of a toxin-antitoxin (TA) module. An endoribonuclease that cleaves 23S rRNA in the sarcin-ricin loop (SRL). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB20.[UniProtKB:P95004][HAMAP-Rule:MF_00265]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	VapBCs, virulence-associated proteins, are the most abundant type II toxin-antitoxin (TA) systems in prokaryotes. Under normal conditions, toxin and antitoxin interact to form a heterooctameric complex, which upon binding to operator sites, inhibits their own expression. Under stress conditions, the VapB antitoxin is degraded by cellular proteases to release a free VapC toxin, which in turn inhibits cell growth mainly by targeting protein translation. However, the intermediate steps involved in the assembly of the heterooctameric complex have not been resolved. Here, we report a 1.75 A resolution crystal structure of VapC20, a Sarcin-Ricin loop cleaving toxin from type II TA system of Mycobacterium tuberculosis. Using analytical ultracentrifugation (AUC) studies, we show that VapC20 exists as a homodimer in solution. The structural analysis of VapC homologs further suggests that VapCs form homodimers. We demonstrate that VapC20 is an obligate homodimer, and its self-association is critical for its folding and activity. Surface plasmon resonance experiments suggest that VapC20 interacts with its cognate antitoxin VapB20 to form a stable complex with nanomolar affinity. A high association rate coupled with a very slow dissociation rate ensures minimal toxicity under normal growth conditions. AUC studies reveal that VapB20 also exists as a homodimer in solution and further associates with VapC20 dimers to form heterotetramers and heterooctamers in a concentration-dependent manner. The results presented here provide valuable insights into the assembly of VapBC family of toxins which is essential for their function and regulation. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly.,Deep A, Kaundal S, Agarwal S, Singh R, Thakur KG FEBS J. 2017 Oct 7. doi: 10.1111/febs.14289. PMID:28986943<ref>PMID:28986943</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5wz4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deep, A]]
		+	[[Category: Thakur, K G]]
		+	[[Category: Homodimer]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pin-domain]]
		+	[[Category: Sarcin-ricin loop cleaving toxin]]
		+	[[Category: Toxin-antitoxin system]]
		+	[[Category: Vapc toxin]]

OCA at 15:12, 27 September 2017

OCA — Wed, 27 Sep 2017 15:12:19 GMT

←Older revision		Revision as of 15:12, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wz4 is ON HOLD	+	The entry 5wz4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5wz4" [edit=sysop:move=sysop]

OCA — Wed, 25 Jan 2017 22:37:05 GMT

Protected "5wz4" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:37, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5wz4 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Jan 2017 22:37:04 GMT

New page: '''Unreleased structure''' The entry 5wz4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5wz4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]