OCA at 14:45, 18 October 2023

OCA — Wed, 18 Oct 2023 14:45:05 GMT

←Older revision		Revision as of 14:45, 18 October 2023
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-	====	+	==Rev1 Ternary Complex with dCTP and Ca2+==
-	<StructureSection load='6x6z' size='340' side='right'caption='[[6x6z]]' scene=''>	+	<StructureSection load='6x6z' size='340' side='right'caption='[[6x6z]], [[Resolution\|resolution]] 1.40Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6x6z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] 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=6X6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X6Z 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=6x6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x6z OCA], [~~http~~://pdbe.org/6x6z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6x6z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6x6z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6x6z 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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6x6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x6z OCA], [https://pdbe.org/6x6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x6z RCSB], [https://www.ebi.ac.uk/pdbsum/6x6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x6z ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During DNA replication, replicative DNA polymerases may encounter DNA lesions, which can stall replication forks. One way to prevent replication fork stalling is through the recruitment of specialized translesion synthesis (TLS) polymerases that have evolved to incorporate nucleotides opposite DNA lesions. Rev1 is a specialized TLS polymerase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts. Lesion bypass is accomplished using a unique protein-template mechanism in which the templating base is evicted from the DNA helix and the incoming dCTP hydrogen bonds with an arginine side chain of Rev1. To understand the protein-template mechanism at an atomic level, we employed a combination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on the Saccharomyces cerevisiae Rev1 protein. We find that Rev1 evicts the templating base from the DNA helix prior to binding the incoming nucleotide. Binding the incoming nucleotide changes the conformation of the DNA substrate to orient it for nucleotidyl transfer, although this is not coupled to large structural changes in Rev1 like those observed with other DNA polymerases. Moreover, we found that following nucleotide incorporation, Rev1 converts the pyrophosphate product to two monophosphates, which drives the reaction in the forward direction and prevents pyrophosphorolysis. Following nucleotide incorporation, the hydrogen bonds between the incorporated nucleotide and the arginine side chain are broken, but the templating base remains extrahelical. These postcatalytic changes prevent potentially mutagenic processive synthesis by Rev1 and facilitate dissociation of the DNA product from the enzyme.
		+
		+	Visualizing Rev1 catalyze protein-template DNA synthesis.,Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25494-25504. doi:, 10.1073/pnas.2010484117. Epub 2020 Sep 30. PMID:32999062<ref>PMID:32999062</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6x6z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Freudenthal BD]]
		+	[[Category: Weaver TM]]

OCA at 07:10, 30 September 2020

OCA — Wed, 30 Sep 2020 07:10:23 GMT

←Older revision		Revision as of 07:10, 30 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6x6z ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6x6z' size='340' side='right'caption='[[6x6z]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= 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=6x6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x6z OCA], [http://pdbe.org/6x6z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6x6z RCSB], [http://www.ebi.ac.uk/pdbsum/6x6z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6x6z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 06:31, 22 July 2020

OCA — Wed, 22 Jul 2020 06:31:58 GMT

←Older revision		Revision as of 06:31, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6x6z is ON HOLD	+	The entry 6x6z is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6x6z" [edit=sysop:move=sysop]

OCA — Wed, 10 Jun 2020 04:56:32 GMT

Protected "6x6z" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:56, 10 June 2020

OCA: New page: '''Unreleased structure''' The entry 6x6z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Jun 2020 04:56:31 GMT

New page: '''Unreleased structure''' The entry 6x6z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6x6z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6x6z - Revision history

OCA at 14:45, 18 October 2023

OCA at 07:10, 30 September 2020

OCA at 06:31, 22 July 2020

OCA: Protected "6x6z" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6x6z is ON HOLD Authors: Description: Category: Unreleased Structures