3ihq - Revision history

OCA at 07:47, 6 September 2023

2023-09-06T07:47:58Z

←Older revision		Revision as of 07:47, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3ihq' size='340' side='right'caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3ihq' size='340' side='right'caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1z3e\|1z3e]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>BSU11500, spxA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835]), BSU01430, rpoA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [https://pdbe.org/3ihq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [https://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq 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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [https://pdbe.org/3ihq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [https://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SPX_BACSU SPX_BACSU]] Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.<ref>PMID:11703662</ref> <ref>PMID:12642660</ref> ~~[[https://www.uniprot.org/uniprot/RPOA_BACSU RPOA_BACSU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.~~	+	[https://www.uniprot.org/uniprot/SPX_BACSU SPX_BACSU] Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.<ref>PMID:11703662</ref> <ref>PMID:12642660</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835]]~~	+	[[Category: Bacillus subtilis]]
-	~~[[Category: DNA-directed RNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brennan~~, R G~~]]	+	[[Category: Brennan RG]]
-	[[Category: Newberry~~, K J]]~~	+	[[Category: Newberry KJ]]
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Dna-directed rna polymerase]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Oxidative stress]]~~	+
-	~~[[Category: Redox-active center]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Spx]]~~	+
-	~~[[Category: Stress response]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription-transferase complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:10, 13 October 2021

2021-10-13T12:10:52Z

←Older revision		Revision as of 12:10, 13 October 2021
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	==Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras==		==Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras==
-	<StructureSection load='3ihq' size='340' side='right' caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3ihq' size='340' side='right'caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z3e\|1z3e]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1z3e\|1z3e]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), BSU01430, rpoA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), BSU01430, rpoA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [~~http~~://pdbe.org/3ihq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq 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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [https://pdbe.org/3ihq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [https://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SPX_BACSU SPX_BACSU]] Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.<ref>PMID:11703662</ref> <ref>PMID:12642660</ref> [[~~http~~://www.uniprot.org/uniprot/RPOA_BACSU RPOA_BACSU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	+	[[https://www.uniprot.org/uniprot/SPX_BACSU SPX_BACSU]] Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.<ref>PMID:11703662</ref> <ref>PMID:12642660</ref> [[https://www.uniprot.org/uniprot/RPOA_BACSU RPOA_BACSU]] 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 33:		Line 33:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Brennan, R G]]		[[Category: Brennan, R G]]
	[[Category: Newberry, K J]]		[[Category: Newberry, K J]]

OCA at 09:56, 19 December 2018

2018-12-19T09:56:05Z

←Older revision		Revision as of 09:56, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='3ihq' size='340' side='right' caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3ihq' size='340' side='right' caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z3e\|1z3e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z3e\|1z3e]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~]), BSU01430, rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), BSU01430, rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [http://pdbe.org/3ihq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [http://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq ProSAT]</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [http://pdbe.org/3ihq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [http://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq ProSAT]</span></td></tr>
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/ih/3ihq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/3ihq_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 38:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Brennan, R G]]		[[Category: Brennan, R G]]
	[[Category: Newberry, K J]]		[[Category: Newberry, K J]]
		+	[[Category: Cytoplasm]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]
	[[Category: Dna-directed rna polymerase]]		[[Category: Dna-directed rna polymerase]]

OCA at 15:08, 5 August 2016

2016-08-05T15:08:17Z

←Older revision		Revision as of 15:08, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras==		==Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras==
	<StructureSection load='3ihq' size='340' side='right' caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3ihq' size='340' side='right' caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z3e\|1z3e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z3e\|1z3e]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~]), BSU01430, rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900]), BSU01430, rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [http://www.ebi.ac.uk/pdbsum/3ihq 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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [http://pdbe.org/3ihq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [http://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq 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=3ihq 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 3ihq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Brennan, R G]]		[[Category: Brennan, R G]]

OCA at 19:49, 25 December 2014

2014-12-25T19:49:22Z

←Older revision		Revision as of 19:49, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3ihq.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras==
		+	<StructureSection load='3ihq' size='340' side='right' caption='[[3ihq]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IHQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z3e\|1z3e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU11500, spxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]), BSU01430, rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [http://www.ebi.ac.uk/pdbsum/3ihq PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SPX_BACSU SPX_BACSU]] Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.<ref>PMID:11703662</ref> <ref>PMID:12642660</ref> [[http://www.uniprot.org/uniprot/RPOA_BACSU RPOA_BACSU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
		+	== 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/ih/3ihq_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 ==
		+	BACKGROUND: Spx, an ArsC (arsenate reductase) family member, is a global transcriptional regulator of the microbial stress response and is highly conserved amongst Gram-positive bacteria. Bacillus subtilis Spx protein exerts positive and negative control of transcription through its interaction with the C-terminal domain of the RNA polymerase (RNAP) alpha subunit (alphaCTD). Spx activates trxA (thioredoxin) and trxB (thioredoxin reductase) in response to thiol stress, and bears an N-terminal C10XXC13 redox disulfide center that is oxidized in active Spx. METHODOLOGY/PRINCIPAL FINDINGS: The structure of mutant Spx(C10S) showed a change in the conformation of helix alpha4. Amino acid substitutions R60E and K62E within and adjacent to helix alpha4 conferred defects in Spx-activated transcription but not Spx-dependent repression. Electrophoretic mobility-shift assays showed alphaCTD interaction with trxB promoter DNA, but addition of Spx generated a supershifted complex that was disrupted in the presence of reductant (DTT). Interaction of alphaCTD/Spx complex with promoter DNA required the cis-acting elements -45AGCA-42 and -34AGCG-31 of the trxB promoter. The Spx(G52R) mutant, defective in alphaCTD binding, did not interact with the alphaCTD-trxB complex. Spx(R60E) not only failed to complex with alphaCTD-trxB, but also disrupted alphaCTD-trxB DNA interaction. CONCLUSIONS/SIGNIFICANCE: The results show that Spx and alphaCTD form a complex that recognizes the promoter DNA of an Spx-controlled gene. A conformational change during oxidation of Spx to the disulfide form likely alters the structure of Spx alpha helix alpha4, which contains residues that function in transcriptional activation and alphaCTD/Spx-promoter interaction. The results suggest that one of these residues, R60 of the alpha4 region of oxidized Spx, functions in alphaCTD/Spx-promoter contact but not in alphaCTD interaction.

-	~~{{STRUCTURE_3ihq\| PDB=3ihq \| SCENE= }}~~	+	Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit.,Nakano MM, Lin A, Zuber CS, Newberry KJ, Brennan RG, Zuber P PLoS One. 2010 Jan 13;5(1):e8664. PMID:20084284<ref>PMID:20084284</ref>

-	~~===Crystal Structure~~ of ~~Reduced C10S Spx in Complex with~~ the ~~Alpha C-terminal Domain of RNA Polymeras===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20084284}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ihq]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020084284<~~/~~ref~~><~~ref group="xtra">PMID:016249335</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
-	[[Category: Brennan, R G.]]	+	[[Category: Brennan, R G]]
-	[[Category: Newberry, K J.]]	+	[[Category: Newberry, K J]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]
	[[Category: Dna-directed rna polymerase]]		[[Category: Dna-directed rna polymerase]]

OCA at 20:45, 20 October 2012

2012-10-20T20:45:10Z

←Older revision		Revision as of 20:45, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3ihq]] is a 2 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].	+	[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].

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

OCA at 11:30, 27 July 2012

2012-07-27T11:30:51Z

←Older revision		Revision as of 11:30, 27 July 2012
Line 1:		Line 1:
	[[Image:3ihq.png\|left\|200px]]		[[Image:3ihq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ihq", 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_3ihq\| PDB=3ihq \| SCENE= }}		{{STRUCTURE_3ihq\| PDB=3ihq \| SCENE= }}

	===Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras===		===Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20084284}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20084284 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20084284}}		{{ABSTRACT_PUBMED_20084284}}

	==About this Structure==		==About this Structure==
-	[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].	+	[[3ihq]] is a 2 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20084284~~</ref><ref group="xtra">PMID:~~16249335~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020084284</ref><ref group="xtra">PMID:016249335</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Brennan, R G.]]		[[Category: Brennan, R G.]]
	[[Category: Newberry, K J.]]		[[Category: Newberry, K J.]]
-	[[Category: Cytoplasm]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]
	[[Category: Dna-directed rna polymerase]]		[[Category: Dna-directed rna polymerase]]
Line 38:		Line 29:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Transcription/transferase complex]]	+	[[Category: Transcription-transferase complex]]
	[[Category: Transferase]]		[[Category: Transferase]]

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

2011-03-14T20:42:52Z

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

←Older revision

Revision as of 20:42, 14 March 2011

OCA at 20:42, 14 March 2011

2011-03-14T20:42:48Z

←Older revision		Revision as of 20:42, 14 March 2011
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3ihq.png\|left\|200px]]
-	[[Image:3ihq.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~3IHQ~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].	+	[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].

	==Reference==		==Reference==
Line 41:		Line 40:
	[[Category: Transcription/transferase complex]]		[[Category: Transcription/transferase complex]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:44:10 2010''

OCA at 07:44, 3 February 2010

2010-02-03T07:44:11Z

←Older revision		Revision as of 07:44, 3 February 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3ihq.jpg\|left\|200px]]

-	The ~~entry 3ihq~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ihq", 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_3ihq\| PDB=3ihq \| SCENE= }}

-	~~Authors: Newberry, K.J., Brennan, R.G.~~	+	===Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras===

-	Description: Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Aug 12 12~~:25:~~45 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20084284}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20084284 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20084284}}
		+
		+	==About this Structure==
		+	3IHQ is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20084284</ref><ref group="xtra">PMID:16249335</ref><references group="xtra"/>
		+	[[Category: Bacillus subtilis]]
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Brennan, R G.]]
		+	[[Category: Newberry, K J.]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Dna-directed rna polymerase]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Oxidative stress]]
		+	[[Category: Redox-active center]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Spx]]
		+	[[Category: Stress response]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Transcription/transferase complex]]
		+	[[Category: Transferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:44:10 2010''