OCA at 14:32, 18 October 2023

OCA — Wed, 18 Oct 2023 14:32:15 GMT

←Older revision		Revision as of 14:32, 18 October 2023
Line 1:		Line 1:

	==Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP==		==Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP==
-	<StructureSection load='6woy' size='340' side='right'caption='[[6woy]]' scene=''>	+	<StructureSection load='6woy' size='340' side='right'caption='[[6woy]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WOY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WOY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6woy]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WOY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6woy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6woy OCA], [~~http~~://pdbe.org/6woy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6woy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6woy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6woy ProSAT]</span></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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH1:3-DEOXY-CYTIDINE-5-TRIPHOSPHATE'>CH1</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=6woy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6woy OCA], [https://pdbe.org/6woy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6woy RCSB], [https://www.ebi.ac.uk/pdbsum/6woy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6woy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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;">
		+	== Publication Abstract from PubMed ==
		+	RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2'dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2'OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2'dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here, we show that a conserved Arg residue uses a two-pronged strategy to select against 2'dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2'OH group to promote NTP binding, but selectively inhibits incorporation of 2'dNTPs by interacting with their 3'OH group to favor the catalytically-inert 2'-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.
		+
		+	The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases.,Makinen JJ, Shin Y, Vieras E, Virta P, Metsa-Ketela M, Murakami KS, Belogurov GA Nat Commun. 2021 Feb 4;12(1):796. doi: 10.1038/s41467-021-21005-w. PMID:33542236<ref>PMID:33542236</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6woy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Thermus thermophilus]]
	[[Category: Murakami KS]]		[[Category: Murakami KS]]
	[[Category: Shin Y]]		[[Category: Shin Y]]

OCA at 06:28, 10 June 2020

OCA — Wed, 10 Jun 2020 06:28:48 GMT

←Older revision		Revision as of 06:28, 10 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6woy ~~is ON HOLD~~	+	==Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP==
-		+	<StructureSection load='6woy' size='340' side='right'caption='[[6woy]]' scene=''>
-	~~Authors~~: ~~Shin~~, Y., ~~Murakami~~, K.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WOY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WOY FirstGlance]. <br>
-	~~Description: Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6woy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6woy OCA], [http://pdbe.org/6woy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6woy RCSB], [http://www.ebi.ac.uk/pdbsum/6woy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6woy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Murakami~~, K.S~~]]	+	__TOC__
-	[[Category: Shin, Y]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Murakami KS]]
		+	[[Category: Shin Y]]

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

OCA — Wed, 06 May 2020 04:27:51 GMT

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

←Older revision

Revision as of 04:27, 6 May 2020

OCA: New page: '''Unreleased structure''' The entry 6woy is ON HOLD Authors: Shin, Y., Murakami, K.S. Description: Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP [[Cat...

OCA — Wed, 06 May 2020 04:27:50 GMT

New page: '''Unreleased structure''' The entry 6woy is ON HOLD Authors: Shin, Y., Murakami, K.S. Description: Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP [[Cat...

New page

'''Unreleased structure'''

The entry 6woy is ON HOLD

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

Description: Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP
[[Category: Unreleased Structures]]
[[Category: Murakami, K.S]]
[[Category: Shin, Y]]

6woy - Revision history

OCA at 14:32, 18 October 2023

OCA at 06:28, 10 June 2020

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

OCA: New page: '''Unreleased structure''' The entry 6woy is ON HOLD Authors: Shin, Y., Murakami, K.S. Description: Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP [[Cat...