4kmu - Revision history

OCA at 16:01, 20 September 2023

OCA — Wed, 20 Sep 2023 16:01:57 GMT

←Older revision		Revision as of 16:01, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KMU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KMU 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=RFP:RIFAMPICIN'>RFP</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]] 3.85Å</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=RFP:RIFAMPICIN'>RFP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [https://pdbe.org/4kmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [https://www.ebi.ac.uk/pdbsum/4kmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmu 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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [https://pdbe.org/4kmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [https://www.ebi.ac.uk/pdbsum/4kmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:01, 7 December 2022

OCA — Wed, 07 Dec 2022 09:01:16 GMT

←Older revision		Revision as of 09:01, 7 December 2022
Line 1:		Line 1:

	==X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin==		==X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin==
-	<StructureSection load='4kmu' size='340' side='right' caption='[[4kmu]], [[Resolution\|resolution]] 3.85Å' scene=''>	+	<StructureSection load='4kmu' size='340' side='right'caption='[[4kmu]], [[Resolution\|resolution]] 3.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KMU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KMU 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=RFP:RIFAMPICIN'>RFP</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=RFP:RIFAMPICIN'>RFP</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">[[4kn4\|4kn4]], [[4kn7\|4kn7]]</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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [https://pdbe.org/4kmu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [https://www.ebi.ac.uk/pdbsum/4kmu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmu ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [~~http~~://pdbe.org/4kmu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kmu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.	+	[https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==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/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~DNA-directed RNA polymerase~~]]	+	[[Category: Large Structures]]
-	[[Category: Murakami~~, K S]]~~	+	[[Category: Murakami KS]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transferase-antibiotic complex~~]]	+

OCA at 22:16, 5 August 2016

OCA — Fri, 05 Aug 2016 22:16:33 GMT

←Older revision		Revision as of 22:16, 5 August 2016
Line 1:		Line 1:
		+
	==X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin==		==X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin==
	<StructureSection load='4kmu' size='340' side='right' caption='[[4kmu]], [[Resolution\|resolution]] 3.85Å' scene=''>		<StructureSection load='4kmu' size='340' side='right' caption='[[4kmu]], [[Resolution\|resolution]] 3.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KMU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KMU 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=RFP:RIFAMPICIN'>RFP</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"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RFP:RIFAMPICIN'>RFP</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">[[4kn4\|4kn4]], [[4kn7\|4kn7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kn4\|4kn4]], [[4kn7\|4kn7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), rpoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [http://www.ebi.ac.uk/pdbsum/4kmu 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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [http://pdbe.org/4kmu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [http://www.ebi.ac.uk/pdbsum/4kmu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kmu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4kmu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
		+	*[[Sigma factor\|Sigma factor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
-	[[Category: Escherichia coli]]
	[[Category: Murakami, K S]]		[[Category: Murakami, K S]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 22:23, 25 December 2014

OCA — Thu, 25 Dec 2014 22:23:01 GMT

←Older revision		Revision as of 22:23, 25 December 2014
Line 9:		Line 9:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [http://www.ebi.ac.uk/pdbsum/4kmu 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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [http://www.ebi.ac.uk/pdbsum/4kmu PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 15:06, 21 December 2014

OCA — Sun, 21 Dec 2014 15:06:54 GMT

←Older revision		Revision as of 15:06, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4kmu\| PDB=4kmu \| SCENE= }}~~	+	==X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin==
-	===X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin===	+	<StructureSection load='4kmu' size='340' side='right' caption='[[4kmu]], [[Resolution\|resolution]] 3.85Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23679862}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KMU 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=RFP:RIFAMPICIN'>RFP</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">[[4kn4\|4kn4]], [[4kn7\|4kn7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), rpoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=4kmu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kmu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kmu RCSB], [http://www.ebi.ac.uk/pdbsum/4kmu PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rifampin, a semisynthetic rifamycin, is the cornerstone of current tuberculosis treatment. Among many semisynthetic rifamycins, benzoxazinorifamycins have great potential for TB treatment due to their superior affinity for wild-type and rifampin-resistant Mycobacterium tuberculosis RNA polymerases and their reduced hepatic Cyp450 induction activity. In this study, we have determined the crystal structures of the Escherichia coli RNA polymerase complexes with two benzoxazinorifamycins. The ansa-naphthalene moieties of the benzoxazinorifamycins bind in a deep pocket of the beta subunit, blocking the path of the RNA transcript. The C3'-tail of benzoxazinorifamycin fits a cavity between the beta subunit and sigma factor. We propose that in addition to blocking RNA exit, the benzoxazinorifamycin C3'-tail changes the sigma region 3.2 loop position, which influences the template DNA at the active site, thereby reducing the efficiency of transcription initiation. This study supports expansion of structure-activity relationships of benzoxazinorifamycins inhibition of RNA polymerase toward uncovering superior analogues with development potential.

-	~~==Function==~~	+	X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins.,Molodtsov V, Nawarathne IN, Scharf NT, Kirchhoff PD, Showalter HD, Garcia GA, Murakami KS J Med Chem. 2013 Jun 13;56(11):4758-63. doi: 10.1021/jm4004889. Epub 2013 May 31. PMID:23679862<ref>PMID:23679862</ref>
-	~~[[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] 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~~.~~[HAMAP-Rule~~:~~MF_00366] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA~~-~~dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates~~. ~~This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule~~:~~MF_00059] [[http://www~~.~~uniprot.org~~/~~uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates~~.~~[HAMAP-Rule:MF_01322] [[http://www~~.~~uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule~~:~~MF_01321] [[http~~://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4kmu]] is~~ a ~~12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:023679862</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[RNA polymerase\|RNA polymerase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Murakami, K S.]]	+	[[Category: Murakami, K S]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transferase-antibiotic complex]]		[[Category: Transferase-antibiotic complex]]

OCA at 14:29, 3 July 2013

OCA — Wed, 03 Jul 2013 14:29:31 GMT

←Older revision		Revision as of 14:29, 3 July 2013
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4kmu]] is a 12 chain structure with sequence from ~~[http://en.wikipedia.org/wiki/ ] and~~ [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA].	+	[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA].

	==Reference==		==Reference==

OCA at 09:35, 3 July 2013

OCA — Wed, 03 Jul 2013 09:35:26 GMT

←Older revision		Revision as of 09:35, 3 July 2013
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA].	+	[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA].

	==Reference==		==Reference==

OCA at 15:10, 19 June 2013

OCA — Wed, 19 Jun 2013 15:10:04 GMT

←Older revision		Revision as of 15:10, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4kmu\| PDB=4kmu \| SCENE= }}
		+	===X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin===
		+	{{ABSTRACT_PUBMED_23679862}}

-	~~The entry 4kmu~~ is ~~ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

-	~~Authors~~: ~~Murakami, K~~.S.	+	==About this Structure==
		+	[[4kmu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KMU OCA].

-	~~Description~~: X-~~ray crystal structure of the Escherichia coli~~ RNA polymerase in complex ~~with Rifampin~~	+	==Reference==
		+	<ref group="xtra">PMID:023679862</ref><references group="xtra"/><references/>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Murakami, K S.]]
		+	[[Category: Dna]]
		+	[[Category: Rna]]
		+	[[Category: Transcription]]
		+	[[Category: Transferase-antibiotic complex]]

OCA: Protected "4kmu" [edit=sysop:move=sysop]

OCA — Thu, 16 May 2013 07:00:22 GMT

Protected "4kmu" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:00, 16 May 2013

OCA: New page: '''Unreleased structure''' The entry 4kmu is ON HOLD Authors: Murakami, K.S. Description: X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin

OCA — Thu, 16 May 2013 07:00:21 GMT

New page: '''Unreleased structure''' The entry 4kmu is ON HOLD Authors: Murakami, K.S. Description: X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin

New page

'''Unreleased structure'''

The entry 4kmu is ON HOLD

Authors: Murakami, K.S.

Description: X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin