6p71 - Revision history

OCA at 07:24, 11 October 2023

2023-10-11T07:24:15Z

←Older revision		Revision as of 07:24, 11 October 2023
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	<StructureSection load='6p71' size='340' side='right'caption='[[6p71]], [[Resolution\|resolution]] 2.92Å' scene=''>		<StructureSection load='6p71' size='340' side='right'caption='[[6p71]], [[Resolution\|resolution]] 2.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p71]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P71 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P71 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p71]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P71 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=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.92Å</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='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=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6p71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p71 OCA], [~~http~~://pdbe.org/6p71 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p71 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p71 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p71 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=6p71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p71 OCA], [https://pdbe.org/6p71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p71 RCSB], [https://www.ebi.ac.uk/pdbsum/6p71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p71 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[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/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A1J1EUF1_THETH A0A1J1EUF1_THETH]] 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][SAAS:SAAS00387808] [[http://www.uniprot.org/uniprot/SIGA_THET2 SIGA_THET2]] 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.[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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed RNA polymerase~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Murakami~~, K S~~]]	+	[[Category: Murakami KS]]
-	[[Category: Shin, Y]]	+	[[Category: Shin Y]]
-	~~[[Category: Pyrbi]]~~	+
-	~~[[Category: Reiterative transcription]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription-dna-rna complex~~]]	+

OCA at 07:57, 11 March 2020

2020-03-11T07:57:56Z

←Older revision		Revision as of 07:57, 11 March 2020
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	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:03, 5 February 2020

2020-02-05T09:03:33Z

←Older revision		Revision as of 09:03, 5 February 2020
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	== Function ==		== Function ==
	[[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/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A1J1EUF1_THETH A0A1J1EUF1_THETH]] 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][SAAS:SAAS00387808] [[http://www.uniprot.org/uniprot/SIGA_THET2 SIGA_THET2]] 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.[HAMAP-Rule:MF_00963]		[[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/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A1J1EUF1_THETH A0A1J1EUF1_THETH]] 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][SAAS:SAAS00387808] [[http://www.uniprot.org/uniprot/SIGA_THET2 SIGA_THET2]] 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.[HAMAP-Rule:MF_00963]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Reiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains eight poly-G RNA bases synthesized using three C bases in the DNA as a template and extends RNA without displacement of the promoter recognition sigma factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak-trigger-freeze X-ray crystallography. We also performed biochemical assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. Lastly, we determined a structure of a transcript initiation complex at the pyrBI promoter and proposed an alternative mechanism of RNA slippage and extension requiring the sigma dissociation from the core enzyme.
		+
		+	Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.,Shin Y, Hedglin M, Murakami KS Nucleic Acids Res. 2020 Jan 22. pii: 5713455. doi: 10.1093/nar/gkz1221. PMID:31965171<ref>PMID:31965171</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6p71" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:25, 24 July 2019

2019-07-24T06:25:19Z

←Older revision		Revision as of 06:25, 24 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6p71 is ~~ON HOLD~~	+	==X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI promoter==
-		+	<StructureSection load='6p71' size='340' side='right'caption='[[6p71]], [[Resolution\|resolution]] 2.92Å' scene=''>
-	~~Authors~~: ~~Shin~~, Y., ~~Murakami~~, K.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6p71]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P71 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P71 FirstGlance]. <br>
-	~~Description~~: X-~~ray crystal structure~~ of ~~a bacterial reiterative~~ transcription ~~complex~~ of ~~pyrBI promoter~~	+	</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=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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>
-	[[Category: Murakami, K.S]]	+	<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=6p71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p71 OCA], [http://pdbe.org/6p71 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p71 RCSB], [http://www.ebi.ac.uk/pdbsum/6p71 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p71 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[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/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A1J1EUF1_THETH A0A1J1EUF1_THETH]] 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][SAAS:SAAS00387808] [[http://www.uniprot.org/uniprot/SIGA_THET2 SIGA_THET2]] 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.[HAMAP-Rule:MF_00963]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Murakami, K S]]
	[[Category: Shin, Y]]		[[Category: Shin, Y]]
		+	[[Category: Pyrbi]]
		+	[[Category: Reiterative transcription]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-dna-rna complex]]

OCA: Protected "6p71" [edit=sysop:move=sysop]

2019-06-12T04:05:39Z

Protected "6p71" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:05, 12 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p71 is ON HOLD Authors: Shin, Y., Murakami, K.S. Description: X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI pr...

2019-06-12T04:05:37Z

New page: '''Unreleased structure''' The entry 6p71 is ON HOLD Authors: Shin, Y., Murakami, K.S. Description: X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI pr...

New page

'''Unreleased structure'''

The entry 6p71 is ON HOLD

Authors: Shin, Y., Murakami, K.S.

Description: X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI promoter
[[Category: Unreleased Structures]]
[[Category: Murakami, K.S]]
[[Category: Shin, Y]]