5yep - Revision history

OCA at 07:41, 10 April 2019

2019-04-10T07:41:43Z

←Older revision		Revision as of 07:41, 10 April 2019
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	==Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis==		==Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis==
-	<StructureSection load='5yep' size='340' side='right' caption='[[5yep]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5yep' size='340' side='right'caption='[[5yep]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yep]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yep]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEP FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SO_3165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON]), SO_3166 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=5yep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yep OCA], [http://pdbe.org/5yep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yep RCSB], [http://www.ebi.ac.uk/pdbsum/5yep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yep 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=5yep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yep OCA], [http://pdbe.org/5yep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yep RCSB], [http://www.ebi.ac.uk/pdbsum/5yep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yep ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Toxin-antitoxin (TA) loci in bacteria are small genetic modules that regulate various cellular activities, including cell growth and death. The two-gene module encoding a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain have been predicted to represent a novel type II TA system prevalent in archaea and bacteria. However, the neutralization mechanism and cellular targets of the TA family remain unclear. The toxin SO_3166 having a HEPN domain and its cognate antitoxin SO_3165 with an MNT domain constitute a typical type II TA system that regulates cell motility and confers plasmid stability in the bacterium Shewanella oneidensis Here, we report the crystal structure and solution conformation of the SO_3166-SO_3165 pair, representing the first complex structures in this TA family. The structures revealed that SO_3165 and SO_3166 form a tight heterooctamer (at a 2:6 ratio), an organization that is very rare in other TA systems. We also observed that SO_3166 dimerization enables the formation of a deep cleft at the HEPN-domain interface harboring a composite RX4-6H active site that functions as an RNA-cleaving RNase. SO_3165 bound SO_3166 mainly through its two alpha-helices (alpha2 and alpha4), functioning as molecular recognition elements. Moreover, their insertion into the SO_3166 cleft sterically blocked the RX4-6H site or narrowed the cleft to inhibit RNA substrate binding. Structure-based mutagenesis confirmed the important roles of these alpha-helices in SO_3166 binding and inhibition. Our structure-function analysis provides first insights into the neutralization mechanism of the HEPN-MNT TA family.
		+
		+	Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system.,Jia X, Yao J, Gao Z, Liu G, Dong YH, Wang X, Zhang H J Biol Chem. 2018 May 4;293(18):6812-6823. doi: 10.1074/jbc.RA118.002421. Epub, 2018 Mar 19. PMID:29555683<ref>PMID:29555683</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yep" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sheon]]
	[[Category: Dong, Y H]]		[[Category: Dong, Y H]]
	[[Category: Gao, Z Q]]		[[Category: Gao, Z Q]]

OCA at 06:35, 28 March 2018

2018-03-28T06:35:13Z

←Older revision		Revision as of 06:35, 28 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yep is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis==
-		+	<StructureSection load='5yep' size='340' side='right' caption='[[5yep]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Jia~~, X., ~~Gao~~, Z.Q., ~~Zhang, H~~., Dong, Y.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yep]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEP FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis~~	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yep OCA], [http://pdbe.org/5yep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yep RCSB], [http://www.ebi.ac.uk/pdbsum/5yep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yep ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dong, Y H]]
		+	[[Category: Gao, Z Q]]
		+	[[Category: Jia, X]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]
-	[[Category: ~~Dong, Y.H~~]]	+	[[Category: Antitoxin-toxin complex]]
-	[[Category: ~~Gao, Z.Q~~]]	+	[[Category: Hepn-mnt]]
-	[[Category: ~~Jia, X~~]]	+	[[Category: Toxin-antitoxin]]

OCA at 05:55, 21 March 2018

2018-03-21T05:55:36Z

←Older revision		Revision as of 05:55, 21 March 2018
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]
		+	[[Category: Dong, Y.H]]
	[[Category: Gao, Z.Q]]		[[Category: Gao, Z.Q]]
	[[Category: Jia, X]]		[[Category: Jia, X]]
-	[[Category: Dong, Y.H]]

OCA at 05:34, 25 October 2017

2017-10-25T05:34:27Z

←Older revision		Revision as of 05:34, 25 October 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Jia, X., Gao, Z.Q., Zhang, H., Dong, Y.H.		Authors: Jia, X., Gao, Z.Q., Zhang, H., Dong, Y.H.

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

2017-09-27T16:28:52Z

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

←Older revision

Revision as of 16:28, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yep is ON HOLD Authors: Jia, X., Gao, Z.Q., Zhang, H., Dong, Y.H. Description: Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis [[C...

2017-09-27T16:28:51Z

New page: '''Unreleased structure''' The entry 5yep is ON HOLD Authors: Jia, X., Gao, Z.Q., Zhang, H., Dong, Y.H. Description: Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis [[C...

New page

'''Unreleased structure'''

The entry 5yep is ON HOLD

Authors: Jia, X., Gao, Z.Q., Zhang, H., Dong, Y.H.

Description: Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis
[[Category: Unreleased Structures]]
[[Category: Zhang, H]]
[[Category: Gao, Z.Q]]
[[Category: Jia, X]]
[[Category: Dong, Y.H]]