OCA at 15:19, 18 October 2023

2023-10-18T15:19:50Z

←Older revision		Revision as of 15:19, 18 October 2023
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-	====	+	==Human DNA polymerase beta dGDP product complex with Mn2+==
-	<StructureSection load='7k97' size='340' side='right'caption='[[7k97]]' scene=''>	+	<StructureSection load='7k97' size='340' side='right'caption='[[7k97]], [[Resolution\|resolution]] 2.40Å' 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 [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k97]] 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=7K97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K97 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=7k97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k97 OCA], [https://pdbe.org/7k97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k97 RCSB], [https://www.ebi.ac.uk/pdbsum/7k97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k97 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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=7k97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k97 OCA], [https://pdbe.org/7k97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k97 RCSB], [https://www.ebi.ac.uk/pdbsum/7k97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k97 ProSAT]</span></td></tr>
	</table>		</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 ==
		+	DNA polymerases play vital roles in the maintenance and replication of genomic DNA by synthesizing new nucleotide polymers using nucleoside triphosphates as substrates. Deoxynucleoside triphosphates (dNTPs) are the canonical substrates for DNA polymerases; however, some bacterial polymerases have been demonstrated to insert deoxynucleoside diphosphates (dNDPs), which lack a third phosphate group, the gamma-phosphate. Whether eukaryotic polymerases can efficiently incorporate dNDPs has not been investigated, and much about the chemical or structural role played by the gamma-phosphate of dNTPs remains unknown. Using the model mammalian polymerase (Pol) beta, we examine how Pol beta incorporates a substrate lacking a gamma-phosphate [deoxyguanosine diphosphate (dGDP)] utilizing kinetic and crystallographic approaches. Using single-turnover kinetics, we determined dGDP insertion across a templating dC by Pol beta to be drastically impaired when compared to dGTP insertion. We found the most significant impairment in the apparent insertion rate (k(pol)), which was reduced 32000-fold compared to that of dGTP insertion. X-ray crystal structures revealed similar enzyme-substrate contacts for both dGDP and dGTP. These findings suggest the insertion efficiency of dGDP is greatly decreased due to impairments in polymerase chemistry. This work is the first instance of a mammalian polymerase inserting a diphosphate nucleotide and provides insight into the nature of polymerase mechanisms by highlighting how these enzymes have evolved to use triphosphate nucleotide substrates.
		+
		+	Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta.,Varela FA, Freudenthal BD Biochemistry. 2021 Feb 9;60(5):373-380. doi: 10.1021/acs.biochem.0c00847. Epub , 2021 Jan 21. PMID:33475337<ref>PMID:33475337</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k97" 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: Synthetic construct]]
		+	[[Category: Freudenthal BD]]
		+	[[Category: Varela FA]]

OCA at 11:11, 3 February 2021

2021-02-03T11:11:42Z

←Older revision		Revision as of 11:11, 3 February 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7k97 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7k97' size='340' side='right'caption='[[7k97]]' 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=7k97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k97 OCA], [https://pdbe.org/7k97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k97 RCSB], [https://www.ebi.ac.uk/pdbsum/7k97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k97 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:34, 4 November 2020

2020-11-04T05:34:28Z

←Older revision		Revision as of 05:34, 4 November 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k97 is ON HOLD	+	The entry 7k97 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7k97" [edit=sysop:move=sysop]

2020-10-07T04:47:15Z

Protected "7k97" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:47, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7k97 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-10-07T04:47:13Z

New page: '''Unreleased structure''' The entry 7k97 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7k97 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7k97 - Revision history

OCA at 15:19, 18 October 2023

OCA at 11:11, 3 February 2021

OCA at 05:34, 4 November 2020

OCA: Protected "7k97" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7k97 is ON HOLD Authors: Description: Category: Unreleased Structures