3m8k - Revision history

OCA at 21:30, 5 August 2016

OCA — Fri, 05 Aug 2016 21:30:48 GMT

←Older revision		Revision as of 21:30, 5 August 2016
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		+
	==Protein structure of type III plasmid segregation TubZ==		==Protein structure of type III plasmid segregation TubZ==
	<StructureSection load='3m8k' size='340' side='right' caption='[[3m8k]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3m8k' size='340' side='right' caption='[[3m8k]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_thuringiensis Bacillus thuringiensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacti Bacti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M8K 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m89\|3m89]], [[3m8e\|3m8e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m89\|3m89]], [[3m8e\|3m8e]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pBt156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1428 Bacillus thuringiensis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pBt156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1430 BACTI])</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=3m8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m8k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m8k RCSB], [http://www.ebi.ac.uk/pdbsum/3m8k PDBsum]</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=3m8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m8k OCA], [http://pdbe.org/3m8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m8k RCSB], [http://www.ebi.ac.uk/pdbsum/3m8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m8k ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3m8k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3m8k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus thuringiensis~~]]	+	[[Category: Bacti]]
	[[Category: Ni, L]]		[[Category: Ni, L]]
	[[Category: Schumacher, M A]]		[[Category: Schumacher, M A]]

OCA at 16:57, 18 December 2014

OCA — Thu, 18 Dec 2014 16:57:05 GMT

←Older revision		Revision as of 16:57, 18 December 2014
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-	~~{{STRUCTURE_3m8k~~\| ~~PDB~~=3m8k \| ~~SCENE~~= }}	+	==Protein structure of type III plasmid segregation TubZ==
-	===~~Protein~~ structure of ~~type III plasmid segregation TubZ~~===	+	<StructureSection load='3m8k' size='340' side='right' caption='[[3m8k]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20534443}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3m8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M8K 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3m89\|3m89]], [[3m8e\|3m8e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pBt156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1428 Bacillus thuringiensis])</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=3m8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m8k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m8k RCSB], [http://www.ebi.ac.uk/pdbsum/3m8k PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m8/3m8k_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The segregation of plasmid DNA typically requires three elements: a DNA centromere site, an NTPase, and a centromere-binding protein. Because of their simplicity, plasmid partition systems represent tractable models to study the molecular basis of DNA segregation. Unlike eukaryotes, which utilize the GTPase tubulin to segregate DNA, the most common plasmid-encoded NTPases contain Walker-box and actin-like folds. Recently, a plasmid stability cassette on Bacillus thuringiensis pBtoxis encoding a putative FtsZ/tubulin-like NTPase called TubZ and DNA-binding protein called TubR has been described. How these proteins collaborate to impart plasmid stability, however, is unknown. Here we show that the TubR structure consists of an intertwined dimer with a winged helix-turn-helix (HTH) motif. Strikingly, however, the TubR recognition helices mediate dimerization, making canonical HTH-DNA interactions impossible. Mutagenesis data indicate that a basic patch, encompassing the two wing regions and the N termini of the recognition helices, mediates DNA binding, which indicates an unusual HTH-DNA interaction mode in which the N termini of the recognition helices insert into a single DNA groove and the wings into adjacent DNA grooves. The TubZ structure shows that it is as similar structurally to eukaryotic tubulin as it is to bacterial FtsZ. TubZ forms polymers with guanine nucleotide-binding characteristics and polymer dynamics similar to tubulin. Finally, we show that the exposed TubZ C-terminal region interacts with TubR-DNA, linking the TubR-bound pBtoxis to TubZ polymerization. The combined data suggest a mechanism for TubZ-polymer powered plasmid movement.

-	~~==About this Structure==~~	+	Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition.,Ni L, Xu W, Kumaraswami M, Schumacher MA Proc Natl Acad Sci U S A. 2010 Jun 4. PMID:20534443<ref>PMID:20534443</ref>
-	~~[[3m8k]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:020534443</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus thuringiensis]]		[[Category: Bacillus thuringiensis]]
-	[[Category: Ni, L.]]	+	[[Category: Ni, L]]
-	[[Category: Schumacher, M A.]]	+	[[Category: Schumacher, M A]]
	[[Category: Gtp-binding]]		[[Category: Gtp-binding]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]

OCA: Protected "3m8k" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2013 23:32:07 GMT

Protected "3m8k" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:32, 10 April 2013

OCA at 23:32, 10 April 2013

OCA — Wed, 10 Apr 2013 23:32:04 GMT

←Older revision		Revision as of 23:32, 10 April 2013
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-	{{Seed}}
-	[[Image:3m8k.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3m8k", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3m8k\| PDB=3m8k \| SCENE= }}		{{STRUCTURE_3m8k\| PDB=3m8k \| SCENE= }}
-
	===Protein structure of type III plasmid segregation TubZ===		===Protein structure of type III plasmid segregation TubZ===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20534443}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20534443 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20534443}}		{{ABSTRACT_PUBMED_20534443}}

	==About this Structure==		==About this Structure==
-	~~3M8K~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA].	+	[[3m8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20534443~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020534443</ref><references group="xtra"/><references/>
	[[Category: Bacillus thuringiensis]]		[[Category: Bacillus thuringiensis]]
	[[Category: Ni, L.]]		[[Category: Ni, L.]]
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	[[Category: Structural protein]]		[[Category: Structural protein]]
	[[Category: Tubulin-like protein]]		[[Category: Tubulin-like protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 09:53:02 2010''

OCA at 05:46, 21 July 2010

OCA — Wed, 21 Jul 2010 05:46:37 GMT

←Older revision		Revision as of 05:46, 21 July 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3m8k.~~jpg~~\|left\|200px]]	+	[[Image:3m8k.png\|left\|200px]]

	<!--		<!--
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	[[Category: Tubulin-like protein]]		[[Category: Tubulin-like protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul ~~7 08~~:42:18 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 09:53:02 2010''

OCA at 04:36, 7 July 2010

OCA — Wed, 07 Jul 2010 04:36:27 GMT

←Older revision		Revision as of 04:36, 7 July 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3m8k.jpg\|left\|200px]]

-	The ~~entry 3m8k~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3m8k", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3m8k\| PDB=3m8k \| SCENE= }}

-	~~Authors: Schumacher, M.A., Ni, L.~~	+	===Protein structure of type III plasmid segregation TubZ===

-	Description: Protein structure of type III plasmid segregation TubZ

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May~~ ~~5 11~~:38:07 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20534443}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20534443 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20534443}}
		+
		+	==About this Structure==
		+	3M8K is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8K OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20534443</ref><references group="xtra"/>
		+	[[Category: Bacillus thuringiensis]]
		+	[[Category: Ni, L.]]
		+	[[Category: Schumacher, M A.]]
		+	[[Category: Gtp-binding]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Plasmid segregation]]
		+	[[Category: Structural protein]]
		+	[[Category: Tubulin-like protein]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 7 08:42:18 2010''

OCA at 08:38, 5 May 2010

OCA — Wed, 05 May 2010 08:38:07 GMT

←Older revision		Revision as of 08:38, 5 May 2010
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3m8k is ON HOLD	+	The entry 3m8k is ON HOLD until Paper Publication

	Authors: Schumacher, M.A., Ni, L.		Authors: Schumacher, M.A., Ni, L.
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	Description: Protein structure of type III plasmid segregation TubZ		Description: Protein structure of type III plasmid segregation TubZ

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 31 13~~:23:09 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:38:07 2010''

OCA at 10:23, 31 March 2010

OCA — Wed, 31 Mar 2010 10:23:10 GMT

←Older revision		Revision as of 10:23, 31 March 2010
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	Authors: Schumacher, M.A., Ni, L.		Authors: Schumacher, M.A., Ni, L.

-	Description: ~~protein~~ structure of type III plasmid segregation TubZ	+	Description: Protein structure of type III plasmid segregation TubZ

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar ~~24 08~~:39:44 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 31 13:23:09 2010''

OCA: New page: '''Unreleased structure''' The entry 3m8k is ON HOLD Authors: Schumacher, M.A., Ni, L. Description: protein structure of type III plasmid segregation TubZ ''Page seeded by [http://oca...

OCA — Wed, 24 Mar 2010 06:39:44 GMT

New page: '''Unreleased structure''' The entry 3m8k is ON HOLD Authors: Schumacher, M.A., Ni, L. Description: protein structure of type III plasmid segregation TubZ ''Page seeded by [http://oca...

New page

'''Unreleased structure'''

The entry 3m8k is ON HOLD

Authors: Schumacher, M.A., Ni, L.

Description: protein structure of type III plasmid segregation TubZ

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 24 08:39:44 2010''