1ynj - Revision history

OCA at 08:58, 14 February 2024

OCA — Wed, 14 Feb 2024 08:58:27 GMT

←Older revision		Revision as of 08:58, 14 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SRN:SORANGICIN+A'>SRN</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]] 3.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1ynn\|1ynn]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SRN:SORANGICIN+A'>SRN</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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [https://pdbe.org/1ynj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [https://www.ebi.ac.uk/pdbsum/1ynj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynj 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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [https://pdbe.org/1ynj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [https://www.ebi.ac.uk/pdbsum/1ynj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~RPOZ_THEAQ RPOZ_THEAQ~~]~~] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.<ref>PMID:11158566</ref>~~	+	[https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1ynj 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=1ynj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.
-
-	Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase.,Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA EMBO J. 2005 Feb 23;24(4):674-82. Epub 2005 Feb 3. PMID:15692574<ref>PMID:15692574</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ynj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Campbell~~, E A~~]]	+	[[Category: Campbell EA]]
-	[[Category: Darst~~, S A~~]]	+	[[Category: Darst SA]]
-	[[Category: Irschik, H]]	+	[[Category: Irschik H]]
-	[[Category: Jansen, R]]	+	[[Category: Jansen R]]
-	[[Category: Leon, F]]	+	[[Category: Leon F]]
-	[[Category: Pavlova, O]]	+	[[Category: Pavlova O]]
-	[[Category: Severinov, K]]	+	[[Category: Severinov K]]
-	[[Category: Zenkin, N]]	+	[[Category: Zenkin N]]
-	~~[[Category: Transferase~~]]	+

OCA at 16:30, 3 November 2021

OCA — Wed, 03 Nov 2021 16:30:45 GMT

←Older revision		Revision as of 16:30, 3 November 2021
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	<StructureSection load='1ynj' size='340' side='right'caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1ynj' size='340' side='right'caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRN:SORANGICIN+A'>SRN</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=SRN:SORANGICIN+A'>SRN</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">[[1ynn\|1ynn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ynn\|1ynn]]</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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [~~http~~://pdbe.org/1ynj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ynj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynj 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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [https://pdbe.org/1ynj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [https://www.ebi.ac.uk/pdbsum/1ynj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.<ref>PMID:11158566</ref>	+	[[https://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.<ref>PMID:11158566</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:53, 29 January 2020

OCA — Wed, 29 Jan 2020 16:53:06 GMT

←Older revision		Revision as of 16:53, 29 January 2020
Line 1:		Line 1:

	==Taq RNA polymerase-Sorangicin complex==		==Taq RNA polymerase-Sorangicin complex==
-	<StructureSection load='1ynj' size='340' side='right' caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='1ynj' size='340' side='right'caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
	[[Category: Campbell, E A]]		[[Category: Campbell, E A]]

OCA at 06:39, 25 April 2018

OCA — Wed, 25 Apr 2018 06:39:05 GMT

←Older revision		Revision as of 06:39, 25 April 2018
Line 1:		Line 1:
		+
	==Taq RNA polymerase-Sorangicin complex==		==Taq RNA polymerase-Sorangicin complex==
	<StructureSection load='1ynj' size='340' side='right' caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1ynj' size='340' side='right' caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://pdbe.org/1ynj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj 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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://pdbe.org/1ynj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynj ProSAT]</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/yn/1ynj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yn/1ynj_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>
	</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=1ynj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-	*[[Temp1\|Temp1]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:02, 11 September 2015

OCA — Fri, 11 Sep 2015 23:02:05 GMT

←Older revision		Revision as of 23:02, 11 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj 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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://pdbe.org/1ynj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj PDBsum]</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 1ynj" style="background-color:#fffaf0;"></div>

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

OCA at 20:36, 25 December 2014

OCA — Thu, 25 Dec 2014 20:36:23 GMT

←Older revision		Revision as of 20:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRN:SORANGICIN+A'>SRN</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=SRN:SORANGICIN+A'>SRN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj 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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.<ref>PMID:11158566</ref>
	== 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 aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Campbell, E A.]]	+	[[Category: Campbell, E A]]
-	[[Category: Darst, S A.]]	+	[[Category: Darst, S A]]
-	[[Category: Irschik, H.]]	+	[[Category: Irschik, H]]
-	[[Category: Jansen, R.]]	+	[[Category: Jansen, R]]
-	[[Category: Leon, F.]]	+	[[Category: Leon, F]]
-	[[Category: Pavlova, O.]]	+	[[Category: Pavlova, O]]
-	[[Category: Severinov, K.]]	+	[[Category: Severinov, K]]
-	[[Category: Zenkin, N.]]	+	[[Category: Zenkin, N]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 21:44, 28 September 2014

OCA — Sun, 28 Sep 2014 21:44:18 GMT

←Older revision		Revision as of 21:44, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ynj.~~png~~\|~~left~~\|200px]]	+	==Taq RNA polymerase-Sorangicin complex==
		+	<StructureSection load='1ynj' size='340' side='right' caption='[[1ynj]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ynj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YNJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRN:SORANGICIN+A'>SRN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ynn\|1ynn]]</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=1ynj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ynj RCSB], [http://www.ebi.ac.uk/pdbsum/1ynj 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/yn/1ynj_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 ==
		+	A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.

-	~~{{STRUCTURE_1ynj\| PDB=1ynj \| SCENE= }}~~	+	Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase.,Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA EMBO J. 2005 Feb 23;24(4):674-82. Epub 2005 Feb 3. PMID:15692574<ref>PMID:15692574</ref>

-	~~===Taq RNA polymerase-Sorangicin complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15692574}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ynj]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_aquaticus Thermus aquaticus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015692574<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 21:15, 20 October 2012

OCA — Sat, 20 Oct 2012 21:15:57 GMT

←Older revision		Revision as of 21:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ynj]] is a 6 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA].	+	[[1ynj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA].

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

OCA: Protected "1ynj" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 12:53:06 GMT

Protected "1ynj" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:53, 27 July 2012

OCA at 12:53, 27 July 2012

OCA — Fri, 27 Jul 2012 12:53:05 GMT

←Older revision		Revision as of 12:53, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1ynj.png\|left\|200px]]		[[Image:1ynj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ynj", 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_1ynj\| PDB=1ynj \| SCENE= }}		{{STRUCTURE_1ynj\| PDB=1ynj \| SCENE= }}

	===Taq RNA polymerase-Sorangicin complex===		===Taq RNA polymerase-Sorangicin complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15692574}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15692574 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15692574}}		{{ABSTRACT_PUBMED_15692574}}

	==About this Structure==		==About this Structure==
-	~~1YNJ~~ is a 6 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA].	+	[[1ynj]] is a 6 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNJ OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15692574~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015692574</ref><references group="xtra"/>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
Line 35:		Line 26:
	[[Category: Zenkin, N.]]		[[Category: Zenkin, N.]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:27:47 2009''