3hzi - Revision history

OCA at 07:34, 6 September 2023

OCA — Wed, 06 Sep 2023 07:34:12 GMT

←Older revision		Revision as of 07:34, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3hzi' size='340' side='right'caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>		<StructureSection load='3hzi' size='340' side='right'caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HZI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HZI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<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]] 2.98Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dnt\|3dnt]]~~, ~~[[3dnu\|3dnu]], [[3dnv\|3dnv]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">hipA, b1507, JW1500 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), hipB, b1508, JW1501 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [https://pdbe.org/3hzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [https://www.ebi.ac.uk/pdbsum/3hzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hzi ProSAT]</span></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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [https://pdbe.org/3hzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [https://www.ebi.ac.uk/pdbsum/3hzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hzi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. Autophosphorylates (Ser-150) and phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well. The hipA7 mutation leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-type HipA also leads to high antibiotic tolerance of the survivor cells. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>PMID:17041039</ref> <ref>PMID:6348026</ref> <ref>PMID:8021189</ref> <ref>PMID:14622409</ref> <ref>PMID:19150849</ref> [[https://www.uniprot.org/uniprot/HIPB_ECOLI HIPB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA. Binds to operator sites with the consensus sequence 5-'TATCCN(8)GGATA-3' to repress the hipBA operon promoter.	+	[https://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI] Toxic component of a toxin-antitoxin (TA) module. Autophosphorylates (Ser-150) and phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well. The hipA7 mutation leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-type HipA also leads to high antibiotic tolerance of the survivor cells. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>PMID:17041039</ref> <ref>PMID:6348026</ref> <ref>PMID:8021189</ref> <ref>PMID:14622409</ref> <ref>PMID:19150849</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Schumacher~~, M A]]~~	+	[[Category: Schumacher MA]]
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Mdt]]~~	+
-	~~[[Category: Persistence]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 12:06, 13 October 2021

OCA — Wed, 13 Oct 2021 12:06:06 GMT

←Older revision		Revision as of 12:06, 13 October 2021
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	==Structure of mdt protein==		==Structure of mdt protein==
-	<StructureSection load='3hzi' size='340' side='right' caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>	+	<StructureSection load='3hzi' size='340' side='right'caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HZI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HZI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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='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">[[3dnt\|3dnt]], [[3dnu\|3dnu]], [[3dnv\|3dnv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dnt\|3dnt]], [[3dnu\|3dnu]], [[3dnv\|3dnv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hipA, b1507, JW1500 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), hipB, b1508, JW1501 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hipA, b1507, JW1500 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), hipB, b1508, JW1501 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [~~http~~://pdbe.org/3hzi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hzi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hzi ProSAT]</span></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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [https://pdbe.org/3hzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [https://www.ebi.ac.uk/pdbsum/3hzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hzi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. Autophosphorylates (Ser-150) and phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well. The hipA7 mutation leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-type HipA also leads to high antibiotic tolerance of the survivor cells. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>PMID:17041039</ref> <ref>PMID:6348026</ref> <ref>PMID:8021189</ref> <ref>PMID:14622409</ref> <ref>PMID:19150849</ref> [[~~http~~://www.uniprot.org/uniprot/HIPB_ECOLI HIPB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA. Binds to operator sites with the consensus sequence 5-'TATCCN(8)GGATA-3' to repress the hipBA operon promoter.	+	[[https://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. Autophosphorylates (Ser-150) and phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well. The hipA7 mutation leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-type HipA also leads to high antibiotic tolerance of the survivor cells. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>PMID:17041039</ref> <ref>PMID:6348026</ref> <ref>PMID:8021189</ref> <ref>PMID:14622409</ref> <ref>PMID:19150849</ref> [[https://www.uniprot.org/uniprot/HIPB_ECOLI HIPB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA. Binds to operator sites with the consensus sequence 5-'TATCCN(8)GGATA-3' to repress the hipBA operon promoter.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Serine/threonine protein kinase\|Serine/threonine protein kinase]]	+	*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Schumacher, M A]]		[[Category: Schumacher, M A]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 08:15, 12 December 2018

OCA — Wed, 12 Dec 2018 08:15:55 GMT

←Older revision		Revision as of 08:15, 12 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/hz/3hzi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hz/3hzi_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>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3hzi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3hzi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine/threonine protein kinase\|Serine/threonine protein kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:30, 5 August 2016

OCA — Fri, 05 Aug 2016 11:30:29 GMT

←Older revision		Revision as of 11:30, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of mdt protein==		==Structure of mdt protein==
	<StructureSection load='3hzi' size='340' side='right' caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>		<StructureSection load='3hzi' size='340' side='right' caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HZI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HZI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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='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">[[3dnt\|3dnt]], [[3dnu\|3dnu]], [[3dnv\|3dnv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dnt\|3dnt]], [[3dnu\|3dnu]], [[3dnv\|3dnv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hipA, b1507, JW1500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~]), hipB, b1508, JW1501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hipA, b1507, JW1500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), hipB, b1508, JW1501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [http://www.ebi.ac.uk/pdbsum/3hzi 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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [http://pdbe.org/3hzi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [http://www.ebi.ac.uk/pdbsum/3hzi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hzi 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=3hzi 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 3hzi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Schumacher, M A]]		[[Category: Schumacher, M A]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 18:27, 25 December 2014

OCA — Thu, 25 Dec 2014 18:27:41 GMT

←Older revision		Revision as of 18:27, 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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [http://www.ebi.ac.uk/pdbsum/3hzi 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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [http://www.ebi.ac.uk/pdbsum/3hzi PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. Autophosphorylates (Ser-150) and phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well. The hipA7 mutation leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-type HipA also leads to high antibiotic tolerance of the survivor cells. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>PMID:17041039</ref> <ref>PMID:6348026</ref> <ref>PMID:8021189</ref> <ref>PMID:14622409</ref> <ref>PMID:19150849</ref> [[http://www.uniprot.org/uniprot/HIPB_ECOLI HIPB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA. Binds to operator sites with the consensus sequence 5-'TATCCN(8)GGATA-3' to repress the hipBA operon promoter.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 17:12, 18 December 2014

OCA — Thu, 18 Dec 2014 17:12:47 GMT

←Older revision		Revision as of 17:12, 18 December 2014
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-	~~{{STRUCTURE_3hzi~~\| ~~PDB~~=3hzi \| ~~SCENE~~= }}	+	==Structure of mdt protein==
-	===~~Structure of mdt~~ protein===	+	<StructureSection load='3hzi' size='340' side='right' caption='[[3hzi]], [[Resolution\|resolution]] 2.98Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19150849}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hzi]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HZI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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">[[3dnt\|3dnt]], [[3dnu\|3dnu]], [[3dnv\|3dnv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hipA, b1507, JW1500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), hipB, b1508, JW1501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3hzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hzi RCSB], [http://www.ebi.ac.uk/pdbsum/3hzi 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/hz/3hzi_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 ==
		+	Bacterial multidrug tolerance is largely responsible for the inability of antibiotics to eradicate infections and is caused by a small population of dormant bacteria called persisters. HipA is a critical Escherichia coli persistence factor that is normally neutralized by HipB, a transcription repressor, which also regulates hipBA expression. Here, we report multiple structures of HipA and a HipA-HipB-DNA complex. HipA has a eukaryotic serine/threonine kinase-like fold and can phosphorylate the translation factor EF-Tu, suggesting a persistence mechanism via cell stasis. The HipA-HipB-DNA structure reveals the HipB-operator binding mechanism, approximately 70 degrees DNA bending, and unexpected HipA-DNA contacts. Dimeric HipB interacts with two HipA molecules to inhibit its kinase activity through sequestration and conformational inactivation. Combined, these studies suggest mechanisms for HipA-mediated persistence and its neutralization by HipB.

-	~~==Function==~~	+	Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB.,Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG Science. 2009 Jan 16;323(5912):396-401. PMID:19150849<ref>PMID:19150849</ref>
-	~~[[http://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI]] Toxic component~~ of ~~a toxin~~-~~antitoxin (TA) module. Autophosphorylates (Ser-150)~~ and ~~phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well~~. ~~The hipA7 mutation leads to increased generation of persister cells~~, ~~cells that survive antibiotic treatment probably by entering into a dormant state~~. ~~Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires~~ (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-~~type HipA also leads to high antibiotic tolerance of the survivor cells~~. ~~The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>~~PMID:~~17041039</ref><ref>PMID:6348026</ref><ref>PMID:8021189</ref><ref>PMID:14622409</ref>~~<ref>PMID:19150849</ref> [[http://www.uniprot.org/uniprot/HIPB_ECOLI HIPB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA. Binds to operator sites with the consensus sequence 5-'TATCCN(8)GGATA-3' to repress the hipBA operon promoter.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3hzi]] is~~ a ~~3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019150849</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Schumacher, M A.]]	+	[[Category: Schumacher, M A]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Mdt]]		[[Category: Mdt]]

OCA at 09:33, 27 March 2013

OCA — Wed, 27 Mar 2013 09:33:15 GMT

←Older revision		Revision as of 09:33, 27 March 2013
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-	[[Image:3hzi.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3hzi", 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_3hzi\| PDB=3hzi \| SCENE= }}		{{STRUCTURE_3hzi\| PDB=3hzi \| SCENE= }}
-
	===Structure of mdt protein===		===Structure of mdt protein===
		+	{{ABSTRACT_PUBMED_19150849}}

-		+	==Function==
-	<!--	+	[[http://www.uniprot.org/uniprot/HIPA_ECOLI HIPA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. Autophosphorylates (Ser-150) and phosphorylates EF-Tu in vitro (on 'Thr-383'), may act on other proteins as well. The hipA7 mutation leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10-6 to 10-5 whereas mutant hipA7 cells produce persisters at a frequency of 10-2. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA causes cell filamentation and depending on the protein level is toxic enough to reduce cell growth or even kill cells. Expression of wild-type HipA also leads to high antibiotic tolerance of the survivor cells. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter.<ref>PMID:17041039</ref><ref>PMID:6348026</ref><ref>PMID:8021189</ref><ref>PMID:14622409</ref><ref>PMID:19150849</ref> [[http://www.uniprot.org/uniprot/HIPB_ECOLI HIPB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA. Binds to operator sites with the consensus sequence 5-'TATCCN(8)GGATA-3' to repress the hipBA operon promoter.
-	The ~~line below this paragraph~~, ~~{{ABSTRACT_PUBMED_19150849}}, adds the Publication Abstract~~ to ~~the page~~	+
-	(as ~~it appears~~ on ~~PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 19150849 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_19150849}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019150849</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019150849</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Schumacher, M A.]]		[[Category: Schumacher, M A.]]
Line 31:		Line 19:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Transcription/dna complex]]	+	[[Category: Transcription-dna complex]]

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

OCA — Thu, 26 May 2011 11:26:23 GMT

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

←Older revision

Revision as of 11:26, 26 May 2011

OCA at 11:26, 26 May 2011

OCA — Thu, 26 May 2011 11:26:20 GMT

←Older revision		Revision as of 11:26, 26 May 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3hzi.png\|left\|200px]]

-	The ~~entry 3hzi~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3hzi", 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_3hzi\| PDB=3hzi \| SCENE= }}

-	~~Authors: Schumacher, M.A.~~	+	===Structure of mdt protein===

-	Description: Structure of mdt protein

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Jul 15 08~~:28:~~56 2009''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19150849}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19150849 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19150849}}
		+
		+	==About this Structure==
		+	[[3hzi]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dnw 3dnw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HZI OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019150849</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Schumacher, M A.]]
		+	[[Category: Dna-binding]]
		+	[[Category: Mdt]]
		+	[[Category: Persistence]]
		+	[[Category: Repressor]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Transcription/dna complex]]

OCA at 05:28, 15 July 2009

OCA — Wed, 15 Jul 2009 05:28:57 GMT

←Older revision		Revision as of 05:28, 15 July 2009
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	The entry 3hzi is ON HOLD		The entry 3hzi is ON HOLD

-	Authors: Schumacher, M.A~~., Piro, K.M., Xu, W., Hansen, S., Lewis, K., Brennan, R.G~~.	+	Authors: Schumacher, M.A.

-	Description: ~~structure~~ of ~~HipA-HipB-dna-ATP complex~~	+	Description: Structure of mdt protein

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 08:57:53 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 15 08:28:56 2009''