2a69 - Revision history

OCA at 07:19, 23 August 2023

OCA — Wed, 23 Aug 2023 07:19:35 GMT

←Older revision		Revision as of 07:19, 23 August 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A69 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A69 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]~~ </~~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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [https://pdbe.org/2a69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [https://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a69 ProSAT], [https://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [https://pdbe.org/2a69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [https://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a69 ProSAT], [https://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	+	[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	== 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: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Artsimovitch, I]]	+	[[Category: Artsimovitch I]]
-	[[Category: Igarashi, N]]	+	[[Category: Igarashi N]]
-	[[Category: Matsugaki, N]]	+	[[Category: Matsugaki N]]
-	[[Category: Perederina, A]]	+	[[Category: Perederina A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Svetlov D]]
-	[[Category: Svetlov, D]]	+	[[Category: Svetlov V]]
-	[[Category: Svetlov, V]]	+	[[Category: Tahirov TH]]
-	[[Category: Tahirov~~, T H~~]]	+	[[Category: Vassylyev DG]]
-	[[Category: Vassylyev~~, D G~~]]	+	[[Category: Vassylyeva MN]]
-	[[Category: Vassylyeva~~, M N~~]]	+	[[Category: Wakatsuki S]]
-	[[Category: Wakatsuki, S]]	+
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Rifapentin]]~~	+
-	~~[[Category: Rna polymerase holoenzyme]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 14:36, 17 November 2021

OCA — Wed, 17 Nov 2021 14:36:51 GMT

←Older revision		Revision as of 14:36, 17 November 2021
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	<StructureSection load='2a69' size='340' side='right'caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2a69' size='340' side='right'caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2A69 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A69 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [~~http~~://pdbe.org/2a69 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2a69 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [https://pdbe.org/2a69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [https://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a69 ProSAT], [https://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[~~http~~://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[~~http~~://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	+	[[https://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 05:25, 13 February 2020

OCA — Thu, 13 Feb 2020 05:25:15 GMT

←Older revision		Revision as of 05:25, 13 February 2020
Line 1:		Line 1:

	==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin==		==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin==
-	<StructureSection load='2a69' size='340' side='right' caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2a69' size='340' side='right'caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A69 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A69 FirstGlance]. <br>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	*[[Sigma factor\|Sigma factor]]	+	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Artsimovitch, I]]		[[Category: Artsimovitch, I]]

OCA at 07:17, 9 May 2018

OCA — Wed, 09 May 2018 07:17:48 GMT

←Older revision		Revision as of 07:17, 9 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin==		==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin==
	<StructureSection load='2a69' size='340' side='right' caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2a69' size='340' side='right' caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://pdbe.org/2a69 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://pdbe.org/2a69 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2a69 ProSAT], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/2a69_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/2a69_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 15:23, 8 February 2016

OCA — Mon, 08 Feb 2016 15:23:59 GMT

←Older revision		Revision as of 15:23, 8 February 2016
Line 18:		Line 18:
	<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=2a69 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 33:		Line 33:
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
	*[[Sigma factor\|Sigma factor]]		*[[Sigma factor\|Sigma factor]]
-	*[[Temp1\|Temp1]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:55, 10 September 2015

OCA — Thu, 10 Sep 2015 12:55:22 GMT

←Older revision		Revision as of 12:55, 10 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://pdbe.org/2a69 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2a69" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
		+	*[[Sigma factor\|Sigma factor]]
		+	*[[Temp1\|Temp1]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:19, 25 December 2014

OCA — Thu, 25 Dec 2014 00:19:06 GMT

←Older revision		Revision as of 00:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A69 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A69 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</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=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Artsimovitch, I.]]	+	[[Category: Artsimovitch, I]]
-	[[Category: Igarashi, N.]]	+	[[Category: Igarashi, N]]
-	[[Category: Matsugaki, N.]]	+	[[Category: Matsugaki, N]]
-	[[Category: Perederina, A.]]	+	[[Category: Perederina, A]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Svetlov, D.]]	+	[[Category: Svetlov, D]]
-	[[Category: Svetlov, V.]]	+	[[Category: Svetlov, V]]
-	[[Category: Tahirov, T H.]]	+	[[Category: Tahirov, T H]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
-	[[Category: Vassylyeva, M N.]]	+	[[Category: Vassylyeva, M N]]
-	[[Category: Wakatsuki, S.]]	+	[[Category: Wakatsuki, S]]
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Rifapentin]]		[[Category: Rifapentin]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rna polymerase holoenzyme]]		[[Category: Rna polymerase holoenzyme]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:13, 29 September 2014

OCA — Mon, 29 Sep 2014 04:13:10 GMT

←Older revision		Revision as of 04:13, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2a69.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin==
		+	<StructureSection load='2a69' size='340' side='right' caption='[[2a69]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2a69]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A69 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RPT:RIFAPENTINE'>RPT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw7\|1iw7]], [[1smy\|1smy]], [[2a68\|2a68]], [[1a6e\|1a6e]], [[1a6h\|1a6h]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a69 RCSB], [http://www.ebi.ac.uk/pdbsum/2a69 PDBsum], [http://www.topsan.org/Proteins/RSGI/2a69 TOPSAN]</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/a6/2a69_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 ==
		+	Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.

-	~~{{STRUCTURE_2a69\| PDB=2a69 \| SCENE= }}~~	+	Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.,Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG Cell. 2005 Aug 12;122(3):351-63. PMID:16096056<ref>PMID:16096056</ref>

-	~~===Crystal structure~~ of the T. ~~Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16096056}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2a69]] is a 12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016096056<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 10:35, 20 October 2012

OCA — Sat, 20 Oct 2012 10:35:45 GMT

←Older revision		Revision as of 10:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2a69]] is a 12 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA].	+	[[2a69]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A69 OCA].

	==See Also==		==See Also==

OCA: Protected "2a69" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 02:38:37 GMT

Protected "2a69" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:38, 26 July 2012