OCA at 07:56, 11 October 2023

OCA — Wed, 11 Oct 2023 07:56:16 GMT

←Older revision		Revision as of 07:56, 11 October 2023
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	==RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4==		==RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4==
-	<StructureSection load='6uq0' size='340' side='right'caption='[[6uq0]]' scene=''>	+	<StructureSection load='6uq0' size='340' side='right'caption='[[6uq0]], [[Resolution\|resolution]] 3.56Å' 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=6UQ0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6UQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uq0]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UQ0 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=6uq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uq0 OCA], [~~http~~://pdbe.org/6uq0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uq0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uq0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uq0 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]] 3.56Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</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=6uq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uq0 OCA], [https://pdbe.org/6uq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uq0 RCSB], [https://www.ebi.ac.uk/pdbsum/6uq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uq0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oxidation of guanine generates several types of DNA lesions, such as 8-oxoguanine (8OG), 5-guanidinohydantoin (Gh), and spiroiminodihydantoin (Sp). These guanine-derived oxidative DNA lesions interfere with both replication and transcription. However, the molecular mechanism of transcription processing of Gh and Sp remains unknown. In this study, by combining biochemical and structural analysis, we revealed distinct transcriptional processing of these chemically related oxidized lesions: 8OG allows both error-free and error-prone bypass, whereas Gh or Sp causes strong stalling and only allows slow error-prone incorporation of purines. Our structural studies provide snapshots of how polymerase II (Pol II) is stalled by a nonbulky Gh lesion in a stepwise manner, including the initial lesion encounter, ATP binding, ATP incorporation, jammed translocation, and arrested states. We show that while Gh can form hydrogen bonds with adenosine monophosphate (AMP) during incorporation, this base pair hydrogen bonding is not sufficient to hold an ATP substrate in the addition site and is not stable during Pol II translocation after the chemistry step. Intriguingly, we reveal a unique structural reconfiguration of the Gh lesion in which the hydantoin ring rotates approximately 90 degrees and is perpendicular to the upstream base pair planes. The perpendicular hydantoin ring of Gh is stabilized by noncanonical lone pair-pi and CH-pi interactions, as well as hydrogen bonds. As a result, the Gh lesion, as a functional mimic of a 1,2-intrastrand crosslink, occupies canonical -1 and +1 template positions and compromises the loading of the downstream template base. Furthermore, we suggest Gh and Sp lesions are potential targets of transcription-coupled repair.
		+
		+	RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.,Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9338-9348. doi:, 10.1073/pnas.1919904117. Epub 2020 Apr 13. PMID:32284409<ref>PMID:32284409</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6uq0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Synthetic construct]]
	[[Category: Oh J]]		[[Category: Oh J]]
	[[Category: Wang D]]		[[Category: Wang D]]

OCA at 06:27, 10 June 2020

OCA — Wed, 10 Jun 2020 06:27:40 GMT

←Older revision		Revision as of 06:27, 10 June 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6uq0 ~~is ON HOLD until Paper Publication~~	+	==RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4==
-		+	<StructureSection load='6uq0' size='340' side='right'caption='[[6uq0]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UQ0 FirstGlance]. <br>
-	~~Description~~:	+	</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=6uq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uq0 OCA], [http://pdbe.org/6uq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uq0 RCSB], [http://www.ebi.ac.uk/pdbsum/6uq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uq0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Oh J]]
		+	[[Category: Wang D]]

OCA at 13:42, 11 December 2019

OCA — Wed, 11 Dec 2019 13:42:49 GMT

←Older revision		Revision as of 13:42, 11 December 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6uq0 is ON HOLD	+	The entry 6uq0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6uq0" [edit=sysop:move=sysop]

OCA — Wed, 30 Oct 2019 07:39:33 GMT

Protected "6uq0" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:39, 30 October 2019

OCA: New page: '''Unreleased structure''' The entry 6uq0 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Oct 2019 07:39:31 GMT

New page: '''Unreleased structure''' The entry 6uq0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6uq0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6uq0 - Revision history

OCA at 07:56, 11 October 2023

OCA at 06:27, 10 June 2020

OCA at 13:42, 11 December 2019

OCA: Protected "6uq0" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6uq0 is ON HOLD Authors: Description: Category: Unreleased Structures