3cto - Revision history

OCA at 08:23, 20 March 2024

OCA — Wed, 20 Mar 2024 08:23:29 GMT

←Older revision		Revision as of 08:23, 20 March 2024
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	<StructureSection load='3cto' size='340' side='right'caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3cto' size='340' side='right'caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3CTO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CTO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [~~http~~://pdbe.org/3cto PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3cto PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3cto ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [https://pdbe.org/3cto PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [https://www.ebi.ac.uk/pdbsum/3cto PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cto ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RELJ_MYCTU RELJ_MYCTU]] Antitoxin component of a toxin-antitoxin (TA) module. A probable antitoxin for the putative mRNA interferase RelK. Upon expression in E.coli but not in M.smegmatis this protein neutralizes E.coli YoeB. Binds to and represses its own promoter, in combination with RelK repression is somewhat lessened. Several DNA-protein complexes are formed in vitro depending on the RelJ:RelK ratio.	+	[https://www.uniprot.org/uniprot/RELJ_MYCTU RELJ_MYCTU] Antitoxin component of a toxin-antitoxin (TA) module. A probable antitoxin for the putative mRNA interferase RelK. Upon expression in E.coli but not in M.smegmatis this protein neutralizes E.coli YoeB. Binds to and represses its own promoter, in combination with RelK repression is somewhat lessened. Several DNA-protein complexes are formed in vitro depending on the RelJ:RelK ratio.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=3cto 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=3cto ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Toxin-antitoxin modules are present on chromosomes of almost all free-living prokaryotes. Some are implicated to act as stress-responsive elements, among their many functional roles. The YefM-YoeB toxin-antitoxin system is present in many bacterial species, where YefM belongs to the Phd family antidote of phage P1, whereas YoeB is a homolog of the RelE toxin of the RelBE system, rather than the Doc system of phage P1. YoeB, a ribonuclease, is believed to be conformationally stable, whereas YefM has been proposed to be a member of intrinsically disordered proteins. The ribonucleolytic activity of YoeB is neutralized by YefM upon formation of the YefM-YoeB complex. We report here the crystal structure of Mycobacterium tuberculosis YefM from two crystal isoforms. Our crystallographic and biophysical studies reveal that YefM is not an intrinsically unfolded protein and instead forms a well-defined structure with significant secondary and tertiary structure conformations. The residues involved in core formation of the folded structure are evolutionarily conserved among many bacterial species, supporting our observation. The C-terminal end of its polypeptide is highly pliable, which adopts different conformations in different monomers. Since at the physiological level YefM controls the activity of YoeB through intricate protein-protein interactions, the conformational heterogeneity in YefM revealed by our structure suggests that these might act a master switch in controlling YoeB activity.
-
-	Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein.,Kumar P, Issac B, Dodson EJ, Turkenburg JP, Mande SC J Mol Biol. 2008 Nov 14;383(3):482-93. Epub 2008 Sep 4. PMID:18793646<ref>PMID:18793646</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3cto" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dodson, E J~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Issac, B~~]]	+	[[Category: Dodson EJ]]
-	[[Category: ~~Kumar, P~~]]	+	[[Category: Issac B]]
-	[[Category: ~~Mande, S C]]~~	+	[[Category: Kumar P]]
-	~~[[Category: Turkenberg, J~~ P]]	+	[[Category: Mande SC]]
-	[[Category: ~~Homotetramer~~]]	+	[[Category: Turkenberg JP]]
-	[[Category: ~~Toxin inhibitor~~]]	+

OCA at 10:29, 12 August 2020

OCA — Wed, 12 Aug 2020 10:29:42 GMT

←Older revision		Revision as of 10:29, 12 August 2020
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	==Crystal Structure of M. tuberculosis YefM antitoxin==		==Crystal Structure of M. tuberculosis YefM antitoxin==
-	<StructureSection load='3cto' size='340' side='right' caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3cto' size='340' side='right'caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CTO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3CTO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://pdbe.org/3cto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cto ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://pdbe.org/3cto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cto ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dodson, E J]]		[[Category: Dodson, E J]]
	[[Category: Issac, B]]		[[Category: Issac, B]]

OCA at 13:30, 7 November 2018

OCA — Wed, 07 Nov 2018 13:30:44 GMT

←Older revision		Revision as of 13:30, 7 November 2018
Line 1:		Line 1:
		+
	==Crystal Structure of M. tuberculosis YefM antitoxin==		==Crystal Structure of M. tuberculosis YefM antitoxin==
	<StructureSection load='3cto' size='340' side='right' caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3cto' size='340' side='right' caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTO FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://pdbe.org/3cto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto 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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://pdbe.org/3cto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cto ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3cto_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3cto_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 22:44, 7 February 2016

OCA — Sun, 07 Feb 2016 22:44:59 GMT

←Older revision		Revision as of 22:44, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3cto' size='340' side='right' caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3cto' size='340' side='right' caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto 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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://pdbe.org/3cto PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Y3357_MYCTU Y3357_MYCTU~~]] Antitoxin component of a toxin-antitoxin (TA) module. A probable antitoxin for the putative mRNA interferase RelK. Upon expression in E.coli but not in M.smegmatis this protein neutralizes E.coli YoeB.~~<ref>PMID:19114484</ref> <ref>PMID:20011113</ref> <ref>PMID:20498855</ref> <ref>PMID:18793646</ref>~~ Binds to and represses its own promoter, in combination with RelK repression is somewhat lessened. Several DNA-protein complexes are formed in vitro depending on the RelJ:RelK ratio.~~<ref>PMID:19114484</ref> <ref>PMID:20011113</ref> <ref>PMID:20498855</ref> <ref>PMID:18793646</ref>~~	+	[[http://www.uniprot.org/uniprot/RELJ_MYCTU RELJ_MYCTU]] Antitoxin component of a toxin-antitoxin (TA) module. A probable antitoxin for the putative mRNA interferase RelK. Upon expression in E.coli but not in M.smegmatis this protein neutralizes E.coli YoeB. Binds to and represses its own promoter, in combination with RelK repression is somewhat lessened. Several DNA-protein complexes are formed in vitro depending on the RelJ:RelK ratio.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 16:
	<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=3cto ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3cto" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Dodson, E J]]		[[Category: Dodson, E J]]
	[[Category: Issac, B]]		[[Category: Issac, B]]

OCA at 18:41, 24 December 2014

OCA — Wed, 24 Dec 2014 18:41:24 GMT

←Older revision		Revision as of 18:41, 24 December 2014
Line 6:		Line 6:
	<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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto 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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Y3357_MYCTU Y3357_MYCTU]] Antitoxin component of a toxin-antitoxin (TA) module. A probable antitoxin for the putative mRNA interferase RelK. Upon expression in E.coli but not in M.smegmatis this protein neutralizes E.coli YoeB.<ref>PMID:19114484</ref> <ref>PMID:20011113</ref> <ref>PMID:20498855</ref> <ref>PMID:18793646</ref> Binds to and represses its own promoter, in combination with RelK repression is somewhat lessened. Several DNA-protein complexes are formed in vitro depending on the RelJ:RelK ratio.<ref>PMID:19114484</ref> <ref>PMID:20011113</ref> <ref>PMID:20498855</ref> <ref>PMID:18793646</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Dodson, E J.]]	+	[[Category: Dodson, E J]]
-	[[Category: Issac, B.]]	+	[[Category: Issac, B]]
-	[[Category: Kumar, P.]]	+	[[Category: Kumar, P]]
-	[[Category: Mande, S C.]]	+	[[Category: Mande, S C]]
-	[[Category: Turkenberg, J P.]]	+	[[Category: Turkenberg, J P]]
	[[Category: Homotetramer]]		[[Category: Homotetramer]]
	[[Category: Toxin inhibitor]]		[[Category: Toxin inhibitor]]

OCA at 05:59, 10 October 2014

OCA — Fri, 10 Oct 2014 05:59:36 GMT

←Older revision		Revision as of 05:59, 10 October 2014
Line 1:		Line 1:
-	[[~~Image~~:3cto.~~png\|left~~\|200px]]	+	==Crystal Structure of M. tuberculosis YefM antitoxin==
		+	<StructureSection load='3cto' size='340' side='right' caption='[[3cto]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3cto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cto OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cto RCSB], [http://www.ebi.ac.uk/pdbsum/3cto 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/ct/3cto_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 ==
		+	Toxin-antitoxin modules are present on chromosomes of almost all free-living prokaryotes. Some are implicated to act as stress-responsive elements, among their many functional roles. The YefM-YoeB toxin-antitoxin system is present in many bacterial species, where YefM belongs to the Phd family antidote of phage P1, whereas YoeB is a homolog of the RelE toxin of the RelBE system, rather than the Doc system of phage P1. YoeB, a ribonuclease, is believed to be conformationally stable, whereas YefM has been proposed to be a member of intrinsically disordered proteins. The ribonucleolytic activity of YoeB is neutralized by YefM upon formation of the YefM-YoeB complex. We report here the crystal structure of Mycobacterium tuberculosis YefM from two crystal isoforms. Our crystallographic and biophysical studies reveal that YefM is not an intrinsically unfolded protein and instead forms a well-defined structure with significant secondary and tertiary structure conformations. The residues involved in core formation of the folded structure are evolutionarily conserved among many bacterial species, supporting our observation. The C-terminal end of its polypeptide is highly pliable, which adopts different conformations in different monomers. Since at the physiological level YefM controls the activity of YoeB through intricate protein-protein interactions, the conformational heterogeneity in YefM revealed by our structure suggests that these might act a master switch in controlling YoeB activity.

-	~~{{STRUCTURE_3cto\| PDB=3cto \| SCENE= }}~~	+	Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein.,Kumar P, Issac B, Dodson EJ, Turkenburg JP, Mande SC J Mol Biol. 2008 Nov 14;383(3):482-93. Epub 2008 Sep 4. PMID:18793646<ref>PMID:18793646</ref>

-	~~===Crystal Structure~~ of M. ~~tuberculosis YefM antitoxin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18793646}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[3cto]] is a 5 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA].~~	+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Dodson, E J.]]		[[Category: Dodson, E J.]]

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

OCA — Mon, 07 Jan 2013 19:24:00 GMT

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

←Older revision

Revision as of 19:24, 7 January 2013

OCA at 19:23, 7 January 2013

OCA — Mon, 07 Jan 2013 19:23:58 GMT

←Older revision		Revision as of 19:23, 7 January 2013
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-	{{Seed}}
	[[Image:3cto.png\|left\|200px]]		[[Image:3cto.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3cto", 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_3cto\| PDB=3cto \| SCENE= }}		{{STRUCTURE_3cto\| PDB=3cto \| SCENE= }}

	===Crystal Structure of M. tuberculosis YefM antitoxin===		===Crystal Structure of M. tuberculosis YefM antitoxin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18793646}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18793646 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18793646}}		{{ABSTRACT_PUBMED_18793646}}

	==About this Structure==		==About this Structure==
-	~~3CTO~~ is a 5 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA].	+	[[3cto]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA].
-		+
-	~~==Reference==~~	+
-	Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein., Kumar P, Issac B, Dodson EJ, Turkenburg JP, Mande SC, J Mol Biol. 2008 Nov 14;383(3):482-93. Epub 2008 Sep 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18793646 18793646]	+
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Dodson, E J.]]		[[Category: Dodson, E J.]]
Line 32:		Line 17:
	[[Category: Homotetramer]]		[[Category: Homotetramer]]
	[[Category: Toxin inhibitor]]		[[Category: Toxin inhibitor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 10 15:44:48 2008''

OCA at 13:44, 10 December 2008

OCA — Wed, 10 Dec 2008 13:44:48 GMT

←Older revision		Revision as of 13:44, 10 December 2008
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3cto.~~jpg~~\|left\|200px]]	+	[[Image:3cto.png\|left\|200px]]

	<!--		<!--
Line 25:		Line 25:
	Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein., Kumar P, Issac B, Dodson EJ, Turkenburg JP, Mande SC, J Mol Biol. 2008 Nov 14;383(3):482-93. Epub 2008 Sep 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18793646 18793646]		Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein., Kumar P, Issac B, Dodson EJ, Turkenburg JP, Mande SC, J Mol Biol. 2008 Nov 14;383(3):482-93. Epub 2008 Sep 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18793646 18793646]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Dodson, E J.]]
		+	[[Category: Issac, B.]]
		+	[[Category: Kumar, P.]]
		+	[[Category: Mande, S C.]]
		+	[[Category: Turkenberg, J P.]]
	[[Category: Homotetramer]]		[[Category: Homotetramer]]
	[[Category: Toxin inhibitor]]		[[Category: Toxin inhibitor]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri~~ Dec ~~5 09~~:33:55 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 10 15:44:48 2008''

OCA at 07:34, 5 December 2008

OCA — Fri, 05 Dec 2008 07:34:15 GMT

←Older revision		Revision as of 07:34, 5 December 2008
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3cto.jpg\|left\|200px]]

-	The ~~entry 3cto~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3cto", 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_3cto\| PDB=3cto \| SCENE= }}

-	~~Authors: Kumar, P., Issac, B., Dodson, E.J., Turkenberg, J.P., Mande, S.C~~.	+	===Crystal Structure of M. tuberculosis YefM antitoxin===

-	Description: Crystal Structure of M. tuberculosis YefM antitoxin

		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18793646}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18793646 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18793646}}

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jun 11~~ 09:34:06 2008''	+	==About this Structure==
		+	3CTO is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTO OCA].
		+
		+	==Reference==
		+	Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein., Kumar P, Issac B, Dodson EJ, Turkenburg JP, Mande SC, J Mol Biol. 2008 Nov 14;383(3):482-93. Epub 2008 Sep 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18793646 18793646]
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
		+	[[Category: Homotetramer]]
		+	[[Category: Toxin inhibitor]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Dec 5 09:33:55 2008''