OCA at 14:45, 18 October 2023

2023-10-18T14:45:29Z

← Older revision		Revision as of 14:45, 18 October 2023
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	====		==Rev1 R518A Ternary Complex with dCTP and Ca2+==
	<StructureSection load='6x77' size='340' side='right'caption='[[6x77]]' scene=''>		<StructureSection load='6x77' size='340' side='right'caption='[[6x77]], [[Resolution\|resolution]] 1.64Å' 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'>[[6x77]] 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=6X77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X77 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=6x77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x77 OCA], [~~http~~://pdbe.org/6x77 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6x77 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6x77 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6x77 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]] 1.64Å</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></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=6x77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x77 OCA], [https://pdbe.org/6x77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x77 RCSB], [https://www.ebi.ac.uk/pdbsum/6x77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x77 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 6x77" 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

2020-09-30T07:10:34Z

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

	~~The entry~~ 6x77 is ~~ON HOLD until Paper Publication~~		====
			<StructureSection load='6x77' size='340' side='right'caption='[[6x77]]' 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=6x77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x77 OCA], [http://pdbe.org/6x77 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6x77 RCSB], [http://www.ebi.ac.uk/pdbsum/6x77 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6x77 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Z-disk]]

OCA at 03:48, 5 August 2020

2020-08-05T03:48:33Z

← Older revision		Revision as of 03:48, 5 August 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6x77 is ON HOLD		The entry 6x77 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6x77" [edit=sysop:move=sysop]

2020-06-10T04:56:56Z

Protected "6x77" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:56, 10 June 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6x77 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-06-10T04:56:55Z

New page: '''Unreleased structure''' The entry 6x77 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6x77 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6x77 - Revision history

OCA at 14:45, 18 October 2023

OCA at 07:10, 30 September 2020

OCA at 03:48, 5 August 2020

OCA: Protected "6x77" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6x77 is ON HOLD Authors: Description: Category: Unreleased Structures