3k33 - Revision history

OCA at 08:08, 6 September 2023

OCA — Wed, 06 Sep 2023 08:08:12 GMT

←Older revision		Revision as of 08:08, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of the Phd-Doc complex==		==Crystal structure of the Phd-Doc complex==
-	<StructureSection load='3k33' size='340' side='right' caption='[[3k33]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3k33' size='340' side='right'caption='[[3k33]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k33]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpp1 Bpp1~~] and [~~http~~://en.wikipedia.org/wiki/~~Miscellaneous_nucleic_acid Miscellaneous nucleic acid~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3K33 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k33]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_P1 Escherichia virus P1] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K33 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 2.4Å</td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Non-Standard_Residue~~\|~~NonStd Res:~~]]~~</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3dd7\|3dd7]], [[3hs2\|3hs2]], [[3hry\|3hry]]</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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [https://pdbe.org/3k33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [https://www.ebi.ac.uk/pdbsum/3k33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k33 ProSAT]</span></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">doc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 BPP1]), phd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 BPP1])</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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [~~http~~://pdbe.org/3k33 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3k33 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3k33 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/DOC_BPP1 DOC_BPP1]] Toxic component of a toxin-antitoxin (TA) module. Overexpression results in inhibition of growth in liquid cultures and a decrease in colony formation by inhibiting translation, stabilizing mRNA and polysomes; these effects are overcome by concomitant expression of antitoxin phd. Binds 70S ribosomes and the 30S ribosomal subunits, the binding site is the same as for the antibiotic hygromycin B. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Doc and phd proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss. Overexpression of doc can induce the mRNA interferase activity of RelE in vivo.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Antitoxin phd binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> [[http://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1]] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>	+	[https://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpp1~~]]	+	[[Category: Escherichia virus P1]]
-	[[Category: ~~Miscellaneous nucleic acid~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Garcia-Pino, A~~]]	+	[[Category: Unidentified]]
-	[[Category: ~~Loris, R]]~~	+	[[Category: Garcia-Pino A]]
-	~~[[Category: Allostery]]~~	+	[[Category: Loris R]]
-	~~[[Category: Antitoxin]]~~	+
-	~~[[Category: Doc]]~~	+
-	~~[[Category: Fic]]~~	+
-	~~[[Category: Intrinsic disorder]]~~	+
-	~~[[Category: Phd]]~~	+
-	~~[[Category: Ribosome inhibitor]]~~	+
-	~~[[Category: Toxin]]~~	+
-	~~[[Category: Toxin~~-~~antitoxin complex~~]]	+
-	[[Category: ~~Transcription regulation~~]]	+

OCA at 09:20, 26 December 2018

OCA — Wed, 26 Dec 2018 09:20:04 GMT

←Older revision		Revision as of 09:20, 26 December 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k3/3k33_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k3/3k33_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 16:16, 5 August 2016

OCA — Fri, 05 Aug 2016 16:16:17 GMT

←Older revision		Revision as of 16:16, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the Phd-Doc complex==		==Crystal structure of the Phd-Doc complex==
	<StructureSection load='3k33' size='340' side='right' caption='[[3k33]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3k33' size='340' side='right' caption='[[3k33]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k33]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_p1 Enterobacteria phage p1~~] and [http://en.wikipedia.org/wiki/~~Unidentified Unidentified~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K33 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k33]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp1 Bpp1] and [http://en.wikipedia.org/wiki/Miscellaneous_nucleic_acid Miscellaneous nucleic acid]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K33 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd7\|3dd7]], [[3hs2\|3hs2]], [[3hry\|3hry]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd7\|3dd7]], [[3hs2\|3hs2]], [[3hry\|3hry]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">doc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 ~~Enterobacteria phage P1~~]), phd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 ~~Enterobacteria phage P1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">doc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 BPP1]), phd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 BPP1])</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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [http://www.ebi.ac.uk/pdbsum/3k33 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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [http://pdbe.org/3k33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [http://www.ebi.ac.uk/pdbsum/3k33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k33 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3k33 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3k33" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage p1~~]]	+	[[Category: Bpp1]]
-	[[Category: ~~Unidentified~~]]	+	[[Category: Miscellaneous nucleic acid]]
	[[Category: Garcia-Pino, A]]		[[Category: Garcia-Pino, A]]
	[[Category: Loris, R]]		[[Category: Loris, R]]

OCA at 03:54, 25 December 2014

OCA — Thu, 25 Dec 2014 03:54:33 GMT

←Older revision		Revision as of 03:54, 25 December 2014
Line 9:		Line 9:
	<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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [http://www.ebi.ac.uk/pdbsum/3k33 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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [http://www.ebi.ac.uk/pdbsum/3k33 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DOC_BPP1 DOC_BPP1]] Toxic component of a toxin-antitoxin (TA) module. Overexpression results in inhibition of growth in liquid cultures and a decrease in colony formation by inhibiting translation, stabilizing mRNA and polysomes; these effects are overcome by concomitant expression of antitoxin phd. Binds 70S ribosomes and the 30S ribosomal subunits, the binding site is the same as for the antibiotic hygromycin B. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Doc and phd proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss. Overexpression of doc can induce the mRNA interferase activity of RelE in vivo.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Antitoxin phd binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> [[http://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1]] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:58, 18 December 2014

OCA — Thu, 18 Dec 2014 16:58:07 GMT

←Older revision		Revision as of 16:58, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3k33~~\| ~~PDB~~=3k33 \| ~~SCENE~~= }}	+	==Crystal structure of the Phd-Doc complex==
-	===~~Crystal~~ structure of the ~~Phd~~-~~Doc complex~~===	+	<StructureSection load='3k33' size='340' side='right' caption='[[3k33]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20603017}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3k33]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1] and [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K33 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd7\|3dd7]], [[3hs2\|3hs2]], [[3hry\|3hry]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">doc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 Enterobacteria phage P1]), phd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 Enterobacteria phage P1])</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=3k33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k33 RCSB], [http://www.ebi.ac.uk/pdbsum/3k33 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/k3/3k33_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 ==
		+	Regulation of the phd/doc toxin-antitoxin operon involves the toxin Doc as co- or derepressor depending on the ratio between Phd and Doc, a phenomenon known as conditional cooperativity. The mechanism underlying this observed behavior is not understood. Here we show that monomeric Doc engages two Phd dimers on two unrelated binding sites. The binding of Doc to the intrinsically disordered C-terminal domain of Phd structures its N-terminal DNA-binding domain, illustrating allosteric coupling between highly disordered and highly unstable domains. This allosteric effect also couples Doc neutralization to the conditional regulation of transcription. In this way, higher levels of Doc tighten repression up to a point where the accumulation of toxin triggers the production of Phd to counteract its action. Our experiments provide the basis for understanding the mechanism of conditional cooperative regulation of transcription typical of toxin-antitoxin modules. This model may be applicable for the regulation of other biological systems.

-	~~==Function==~~	+	Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity.,Garcia-Pino A, Balasubramanian S, Wyns L, Gazit E, De Greve H, Magnuson RD, Charlier D, van Nuland NA, Loris R Cell. 2010 Jul 9;142(1):101-11. PMID:20603017<ref>PMID:20603017</ref>
-	~~[[http://www.uniprot.org/uniprot/DOC_BPP1 DOC_BPP1]] Toxic component of a toxin-antitoxin (TA) module. Overexpression results in inhibition of growth in liquid cultures~~ and ~~a decrease in colony formation by inhibiting translation, stabilizing mRNA and polysomes; these effects are overcome~~ by ~~concomitant expression of antitoxin phd~~. ~~Binds 70S ribosomes and the 30S ribosomal subunits~~, ~~the binding site is the same as for the antibiotic hygromycin B. Bacteriophage P1 lysogenizes bacteria as a low~~-~~copy number plasmid~~. Doc and phd proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss. Overexpression of doc can induce the mRNA interferase activity of RelE in vivo.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Antitoxin phd binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> [[http://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1]] Antitoxin component of a toxin-antitoxin (TA) ~~module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low~~-~~copy number plasmid~~. ~~Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>~~PMID:9829946</ref> <ref>PMID:18398006</ref> Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:~~18398006~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3k33]] is~~ a ~~5 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1] and [http://en~~.~~wikipedia.org~~/~~wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020603017</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage p1]]		[[Category: Enterobacteria phage p1]]
	[[Category: Unidentified]]		[[Category: Unidentified]]
-	[[Category: Garcia-Pino, A.]]	+	[[Category: Garcia-Pino, A]]
-	[[Category: Loris, R.]]	+	[[Category: Loris, R]]
	[[Category: Allostery]]		[[Category: Allostery]]
	[[Category: Antitoxin]]		[[Category: Antitoxin]]

OCA: Protected "3k33" [edit=sysop:move=sysop]

OCA — Thu, 04 Apr 2013 02:48:24 GMT

Protected "3k33" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:48, 4 April 2013

OCA at 02:48, 4 April 2013

OCA — Thu, 04 Apr 2013 02:48:14 GMT

←Older revision		Revision as of 02:48, 4 April 2013
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-	{{Seed}}
-	[[Image:3k33.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3k33", 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_3k33\| PDB=3k33 \| SCENE= }}		{{STRUCTURE_3k33\| PDB=3k33 \| SCENE= }}
-
	===Crystal structure of the Phd-Doc complex===		===Crystal structure of the Phd-Doc complex===
		+	{{ABSTRACT_PUBMED_20603017}}

-		+	==Function==
-	<!--	+	[[http://www.uniprot.org/uniprot/DOC_BPP1 DOC_BPP1]] Toxic component of a toxin-antitoxin (TA) module. Overexpression results in inhibition of growth in liquid cultures and a decrease in colony formation by inhibiting translation, stabilizing mRNA and polysomes; these effects are overcome by concomitant expression of antitoxin phd. Binds 70S ribosomes and the 30S ribosomal subunits, the binding site is the same as for the antibiotic hygromycin B. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Doc and phd proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss. Overexpression of doc can induce the mRNA interferase activity of RelE in vivo.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Antitoxin phd binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> [[http://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1]] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_20603017}}~~, ~~adds~~ the ~~Publication Abstract~~ to the ~~page~~	+
-	(as ~~it appears~~ on ~~PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 20603017 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_20603017}}~~	+

	==About this Structure==		==About this Structure==
-	~~3K33~~ is a 5 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1] and [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA].	+	[[3k33]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1] and [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20603017~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020603017</ref><references group="xtra"/><references/>
	[[Category: Enterobacteria phage p1]]		[[Category: Enterobacteria phage p1]]
	[[Category: Unidentified]]		[[Category: Unidentified]]
Line 38:		Line 25:
	[[Category: Toxin-antitoxin complex]]		[[Category: Toxin-antitoxin complex]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:42:13 2010''

OCA at 07:34, 18 August 2010

OCA — Wed, 18 Aug 2010 07:34:41 GMT

←Older revision		Revision as of 07:34, 18 August 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3k33.jpg\|left\|200px]]

-	The ~~entry 3k33~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3k33", 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_3k33\| PDB=3k33 \| SCENE= }}

-	~~Authors: Loris, R., Garcia~~-~~Pino, A.~~	+	===Crystal structure of the Phd-Doc complex===

-	Description: Crystal structure of the Phd-Doc complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 28 12~~:56:~~59 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20603017}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20603017 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20603017}}
		+
		+	==About this Structure==
		+	3K33 is a 5 chains structure with sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1] and [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K33 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20603017</ref><references group="xtra"/>
		+	[[Category: Enterobacteria phage p1]]
		+	[[Category: Unidentified]]
		+	[[Category: Garcia-Pino, A.]]
		+	[[Category: Loris, R.]]
		+	[[Category: Allostery]]
		+	[[Category: Antitoxin]]
		+	[[Category: Doc]]
		+	[[Category: Fic]]
		+	[[Category: Intrinsic disorder]]
		+	[[Category: Phd]]
		+	[[Category: Ribosome inhibitor]]
		+	[[Category: Toxin]]
		+	[[Category: Toxin-antitoxin complex]]
		+	[[Category: Transcription regulation]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:42:13 2010''

OCA at 10:57, 28 October 2009

OCA — Wed, 28 Oct 2009 10:57:00 GMT

←Older revision		Revision as of 10:57, 28 October 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3k33 is ON HOLD	+	The entry 3k33 is ON HOLD until Paper Publication

	Authors: Loris, R., Garcia-Pino, A.		Authors: Loris, R., Garcia-Pino, A.
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	Description: Crystal structure of the Phd-Doc complex		Description: Crystal structure of the Phd-Doc complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct ~~14 10~~:07:23 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 28 12:56:59 2009''

OCA at 08:07, 14 October 2009

OCA — Wed, 14 Oct 2009 08:07:24 GMT

←Older revision		Revision as of 08:07, 14 October 2009
Line 3:		Line 3:
	The entry 3k33 is ON HOLD		The entry 3k33 is ON HOLD

-	Authors: Garcia-Pino, ~~Abel , Balasubramanian, Sreeram, Wyns, Lode, Gazit, Ehud, Magnuson, Roy D~~.~~, Charlier, Daniel, Loris, Remy~~	+	Authors: Loris, R., Garcia-Pino, A.

	Description: Crystal structure of the Phd-Doc complex		Description: Crystal structure of the Phd-Doc complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct ~~7 13~~:45:33 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 14 10:07:23 2009''