4oio - Revision history

OCA at 17:14, 20 September 2023

2023-09-20T17:14:44Z

←Older revision		Revision as of 17:14, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OIO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OIO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [https://pdbe.org/4oio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [https://www.ebi.ac.uk/pdbsum/4oio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio 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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [https://pdbe.org/4oio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [https://www.ebi.ac.uk/pdbsum/4oio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:28, 25 January 2023

2023-01-25T07:28:23Z

←Older revision		Revision as of 07:28, 25 January 2023
Line 3:		Line 3:
	<StructureSection load='4oio' size='340' side='right'caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4oio' size='340' side='right'caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Thet8 Thet8] and [http~~://en.wikipedia.org/wiki/~~Thermus_thermophilus~~ Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OIO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [https://pdbe.org/4oio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [https://www.ebi.ac.uk/pdbsum/4oio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD, TTHA0532 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [~~http~~://pdbe.org/4oio PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4oio PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/Q5SKW1_THET8 Q5SKW1_THET8]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth (By similarity).[HAMAP-Rule:MF_00963]	+	[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	<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: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Thermus thermophilus]]	+	[[Category: Thermus thermophilus HB8]]
-	~~[[Category: Thet8~~]]	+	[[Category: Arnold E]]
-	[[Category: Arnold, E]]	+	[[Category: Ebright RH]]
-	[[Category: Ebright~~, R H~~]]	+	[[Category: Zhang Y]]
-	[[Category: Zhang, Y]]	+
-	~~[[Category: De novo transcription initiation]]~~	+
-	~~[[Category: Dna/rna/ntp binding]]~~	+
-	~~[[Category: I site]]~~	+
-	~~[[Category: I+1 site]]~~	+
-	~~[[Category: Nucleoid]]~~	+
-	~~[[Category: Polymerization of ribonucleotide]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Substrate complex]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription initiation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:53, 17 April 2019

2019-04-17T07:53:11Z

←Older revision		Revision as of 07:53, 17 April 2019
Line 1:		Line 1:

	==Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation==		==Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation==
-	<StructureSection load='4oio' size='340' side='right' caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4oio' size='340' side='right'caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OIO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD, TTHA0532 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://pdbe.org/4oio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio 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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://pdbe.org/4oio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio ProSAT]</span></td></tr>
Line 29:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
		+	[[Category: Thet8]]
	[[Category: Arnold, E]]		[[Category: Arnold, E]]
	[[Category: Ebright, R H]]		[[Category: Ebright, R H]]

OCA at 07:24, 5 August 2016

2016-08-05T07:24:00Z

←Older revision		Revision as of 07:24, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation==		==Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation==
	<StructureSection load='4oio' size='340' side='right' caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4oio' size='340' side='right' caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio 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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://pdbe.org/4oio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oio ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4oio" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	*[[Sigma factor\|Sigma factor]]		*[[Sigma factor\|Sigma factor]]
	== References ==		== References ==

OCA at 00:14, 25 December 2014

2014-12-25T00:14:11Z

←Older revision		Revision as of 00:14, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='4oio' size='340' side='right' caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4oio' size='340' side='right' caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. <br>	+	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OIO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio 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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/Q5SKW1_THET8 Q5SKW1_THET8]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth (By similarity).[HAMAP-Rule:MF_00963]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.,Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH Elife. 2014 Jan 1;3:e02450. doi: 10.7554/eLife.02450. PMID:24755292<ref>PMID:24755292</ref>		GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.,Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH Elife. 2014 Jan 1;3:e02450. doi: 10.7554/eLife.02450. PMID:24755292<ref>PMID:24755292</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
		+
		+	==See Also==
		+	*[[Sigma factor\|Sigma factor]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Arnold, E.]]	+	[[Category: Arnold, E]]
-	[[Category: Ebright, R H.]]	+	[[Category: Ebright, R H]]
-	[[Category: Zhang, Y.]]	+	[[Category: Zhang, Y]]
	[[Category: De novo transcription initiation]]		[[Category: De novo transcription initiation]]
	[[Category: Dna/rna/ntp binding]]		[[Category: Dna/rna/ntp binding]]

OCA at 08:14, 7 May 2014

2014-05-07T08:14:58Z

←Older revision		Revision as of 08:14, 7 May 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation==
		+	<StructureSection load='4oio' size='340' side='right' caption='[[4oio]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4oio]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OIO OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oin\|4oin]], [[4oip\|4oip]], [[4oiq\|4oiq]], [[4oir\|4oir]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=4oio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oio OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oio RCSB], [http://www.ebi.ac.uk/pdbsum/4oio PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI: http://dx.doi.org/10.7554/eLife.02450.001.

-	~~The entry 4oio is ON HOLD~~	+	GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.,Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH Elife. 2014 Jan 1;3:e02450. doi: 10.7554/eLife.02450. PMID:24755292<ref>PMID:24755292</ref>

-	~~Authors: Zhang~~, Y., Ebright, R.H., ~~Arnold, E~~.	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure~~ of ~~Thermus thermophilus pre-insertion substrate~~ complex ~~for de novo transcription~~ initiation	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Arnold, E.]]
		+	[[Category: Ebright, R H.]]
		+	[[Category: Zhang, Y.]]
		+	[[Category: De novo transcription initiation]]
		+	[[Category: Dna/rna/ntp binding]]
		+	[[Category: I site]]
		+	[[Category: I+1 site]]
		+	[[Category: Nucleoid]]
		+	[[Category: Polymerization of ribonucleotide]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Substrate complex]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription initiation]]
		+	[[Category: Transferase]]

OCA at 10:29, 5 February 2014

2014-02-05T10:29:48Z

←Older revision		Revision as of 10:29, 5 February 2014
Line 3:		Line 3:
	The entry 4oio is ON HOLD		The entry 4oio is ON HOLD

-	Authors: Zhang, Y., Ebright, R.H, Arnold, E.	+	Authors: Zhang, Y., Ebright, R.H., Arnold, E.

	Description: Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation		Description: Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation

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

2014-01-29T07:10:05Z

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

←Older revision

Revision as of 07:10, 29 January 2014

OCA: New page: '''Unreleased structure''' The entry 4oio is ON HOLD Authors: Zhang, Y., Ebright, R.H, Arnold, E. Description: Crystal structure of Thermus thermophilus pre-insertion substrate complex...

2014-01-29T07:10:03Z

New page: '''Unreleased structure''' The entry 4oio is ON HOLD Authors: Zhang, Y., Ebright, R.H, Arnold, E. Description: Crystal structure of Thermus thermophilus pre-insertion substrate complex...

New page

'''Unreleased structure'''

The entry 4oio is ON HOLD

Authors: Zhang, Y., Ebright, R.H, Arnold, E.

Description: Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation