OCA at 15:31, 18 October 2023

OCA — Wed, 18 Oct 2023 15:31:19 GMT

←Older revision		Revision as of 15:31, 18 October 2023
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-	====	+	==DNA Polymerase Mu, dGTP:At Pre-Catalytic Ground State Ternary Complex, 10 mM Ca2+ (960min)==
-	<StructureSection load='7ksz' size='340' side='right'caption='[[7ksz]]' scene=''>	+	<StructureSection load='7ksz' size='340' side='right'caption='[[7ksz]], [[Resolution\|resolution]] 1.42Å' 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 [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ksz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KSZ FirstGlance]. <br>
-	</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=7ksz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ksz OCA], [https://pdbe.org/7ksz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ksz RCSB], [https://www.ebi.ac.uk/pdbsum/7ksz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ksz 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]] 1.417Å</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7ksz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ksz OCA], [https://pdbe.org/7ksz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ksz RCSB], [https://www.ebi.ac.uk/pdbsum/7ksz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ksz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPOLM_HUMAN DPOLM_HUMAN] Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination.<ref>PMID:12640116</ref> <ref>PMID:12888504</ref> <ref>PMID:17483519</ref> <ref>PMID:17915942</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oxidized dGTP (8-oxo-7,8-dihydro-2 -deoxyguanosine triphosphate, 8-oxodGTP) insertion by DNA polymerases strongly promotes cancer and human disease. How DNA polymerases discriminate against oxidized and undamaged nucleotides, especially in error-prone double strand break (DSB) repair, is poorly understood. High-resolution time-lapse X-ray crystallography snapshots of DSB repair polymerase mu undergoing DNA synthesis reveal that a third active site metal promotes insertion of oxidized and undamaged dGTP in the canonical anti-conformation opposite template cytosine. The product metal bridged O8 with product oxygens, and was not observed in the syn-conformation opposite template adenine (At). Rotation of At into the syn-conformation enabled undamaged dGTP misinsertion. Exploiting metal and substrate dynamics in a rigid active site allows 8-oxodGTP to circumvent polymerase fidelity safeguards to promote pro-mutagenic double strand break repair.
		+
		+	Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide.,Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH Nat Commun. 2021 Apr 6;12(1):2059. doi: 10.1038/s41467-021-21354-6. PMID:33824325<ref>PMID:33824325</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ksz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Jamsen JA]]
		+	[[Category: Wilson SH]]

OCA at 07:28, 19 January 2022

OCA — Wed, 19 Jan 2022 07:28:22 GMT

←Older revision		Revision as of 07:28, 19 January 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7ksz ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7ksz' size='340' side='right'caption='[[7ksz]]' 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 [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7ksz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ksz OCA], [https://pdbe.org/7ksz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ksz RCSB], [https://www.ebi.ac.uk/pdbsum/7ksz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ksz ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:26, 30 December 2020

OCA — Wed, 30 Dec 2020 05:26:30 GMT

←Older revision		Revision as of 05:26, 30 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ksz is ON HOLD	+	The entry 7ksz is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ksz" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2020 05:52:05 GMT

Protected "7ksz" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:52, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7ksz is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Dec 2020 05:52:03 GMT

New page: '''Unreleased structure''' The entry 7ksz is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ksz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7ksz - Revision history

OCA at 15:31, 18 October 2023

OCA at 07:28, 19 January 2022

OCA at 05:26, 30 December 2020

OCA: Protected "7ksz" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7ksz is ON HOLD Authors: Description: Category: Unreleased Structures