OCA at 13:02, 1 November 2023

2023-11-01T13:02:23Z

←Older revision		Revision as of 13:02, 1 November 2023
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-	'''Unreleased structure'''

-	The ~~entry~~ 8b76 is ~~ON HOLD until Paper~~ Publication	+	==The crystal structure of M644G variant of DNA Pol Epsilon containing dTTP in the polymerase active site==
		+	<StructureSection load='8b76' size='340' side='right'caption='[[8b76]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8b76]] is a 6 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=8B76 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B76 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=8b76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b76 OCA], [https://pdbe.org/8b76 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b76 RCSB], [https://www.ebi.ac.uk/pdbsum/8b76 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b76 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPOE_YEAST DPOE_YEAST] DNA polymerase epsilon (DNA polymerase II) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair.<ref>PMID:12124389</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2'-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.

-	~~Authors: Parkash~~, V., ~~Johansson~~, E.	+	A sensor complements the steric gate when DNA polymerase Ïµ discriminates ribonucleotides.,Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E Nucleic Acids Res. 2023 Oct 11:gkad817. doi: 10.1093/nar/gkad817. PMID:37819038<ref>PMID:37819038</ref>

-	~~Description: The crystal structure of M644G variant~~ of ~~DNA Pol Epsilon containing dTTP in~~ the ~~polymerase active site~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Parkash, V~~]]	+	<div class="pdbe-citations 8b76" style="background-color:#fffaf0;"></div>
-	[[Category: Johansson, E]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Johansson E]]
		+	[[Category: Parkash V]]

OCA: Protected "8b76" [edit=sysop:move=sysop]

2022-10-19T16:48:56Z

Protected "8b76" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:48, 19 October 2022

OCA: New page: '''Unreleased structure''' The entry 8b76 is ON HOLD until Paper Publication Authors: Parkash, V., Johansson, E. Description: The crystal structure of M644G variant of DNA Pol Epsilon ...

2022-10-19T16:48:55Z

New page: '''Unreleased structure''' The entry 8b76 is ON HOLD until Paper Publication Authors: Parkash, V., Johansson, E. Description: The crystal structure of M644G variant of DNA Pol Epsilon ...

New page

'''Unreleased structure'''

The entry 8b76 is ON HOLD until Paper Publication

Authors: Parkash, V., Johansson, E.

Description: The crystal structure of M644G variant of DNA Pol Epsilon containing dTTP in the polymerase active site
[[Category: Unreleased Structures]]
[[Category: Parkash, V]]
[[Category: Johansson, E]]

8b76 - Revision history

OCA at 13:02, 1 November 2023

OCA: Protected "8b76" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8b76 is ON HOLD until Paper Publication Authors: Parkash, V., Johansson, E. Description: The crystal structure of M644G variant of DNA Pol Epsilon ...