OCA at 08:38, 9 May 2024

OCA — Thu, 09 May 2024 08:38:50 GMT

←Older revision		Revision as of 08:38, 9 May 2024
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-	'''Unreleased structure'''

-	~~The entry~~ 8vfg is ~~ON HOLD~~	+	==Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC==
		+	<StructureSection load='8vfg' size='340' side='right'caption='[[8vfg]], [[Resolution\|resolution]] 1.54Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8vfg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=8VFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8VFG 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]] 1.54Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8NI:N-[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine'>8NI</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=8vfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8vfg OCA], [https://pdbe.org/8vfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8vfg RCSB], [https://www.ebi.ac.uk/pdbsum/8vfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8vfg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N6-(2-deoxy-alpha,beta-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (FapydG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). FapydG preferentially gives rise to G --> T transversions and G --> A transitions. However, the molecular basis by which FapydG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase beta (Pol beta), a model mammalian polymerase, bypasses a templating FapydG, inserts FapydGTP, and extends from FapydG at the primer terminus. When FapydG is present in the template, Pol beta incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that FapydGTP is a poor substrate but is incorporated approximately 3-times more efficiently opposite dA than dC. Extension from FapydG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of FapydG is likely to be the source of the mutagenic effects of the lesion and not FapydGTP. These experiments increase our understanding of the promutagenic effects of FapydG.

-	~~Authors: Oden, P.N~~., Ryan, ~~B.J.~~, Freudenthal, B.D.	+	Biochemical and structural characterization of Fapy*dG replication by Human DNA polymerase beta.,Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM Nucleic Acids Res. 2024 Apr 18:gkae277. doi: 10.1093/nar/gkae277. PMID:38634780<ref>PMID:38634780</ref>

-	~~Description: Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with~~ a dC	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Ryan, B.J~~]]	+	<div class="pdbe-citations 8vfg" style="background-color:#fffaf0;"></div>
-	[[Category: Freudenthal~~, B.D~~]]	+	== References ==
-	[[Category: Oden~~, P.N~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Freudenthal BD]]
		+	[[Category: Oden PN]]
		+	[[Category: Ryan BJ]]

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

OCA — Wed, 27 Dec 2023 22:17:28 GMT

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

←Older revision

Revision as of 22:17, 27 December 2023

OCA: New page: '''Unreleased structure''' The entry 8vfg is ON HOLD Authors: Oden, P.N., Ryan, B.J., Freudenthal, B.D. Description: Binary DNA Polymerase Beta bound to DNA containing primer terminal ...

OCA — Wed, 27 Dec 2023 22:17:27 GMT

New page: '''Unreleased structure''' The entry 8vfg is ON HOLD Authors: Oden, P.N., Ryan, B.J., Freudenthal, B.D. Description: Binary DNA Polymerase Beta bound to DNA containing primer terminal ...

New page

'''Unreleased structure'''

The entry 8vfg is ON HOLD

Authors: Oden, P.N., Ryan, B.J., Freudenthal, B.D.

Description: Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC
[[Category: Unreleased Structures]]
[[Category: Ryan, B.J]]
[[Category: Freudenthal, B.D]]
[[Category: Oden, P.N]]

8vfg - Revision history

OCA at 08:38, 9 May 2024

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

OCA: New page: '''Unreleased structure''' The entry 8vfg is ON HOLD Authors: Oden, P.N., Ryan, B.J., Freudenthal, B.D. Description: Binary DNA Polymerase Beta bound to DNA containing primer terminal ...