OCA at 16:06, 18 October 2023

OCA — Wed, 18 Oct 2023 16:06:42 GMT

←Older revision		Revision as of 16:06, 18 October 2023
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-	====	+	==Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 0 s==
-	<StructureSection load='7m7y' size='340' side='right'caption='[[7m7y]]' scene=''>	+	<StructureSection load='7m7y' size='340' side='right'caption='[[7m7y]], [[Resolution\|resolution]] 1.80Å' 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'>[[7m7y]] is a 3 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=7M7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7M7Y 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=7m7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m7y OCA], [https://pdbe.org/7m7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m7y RCSB], [https://www.ebi.ac.uk/pdbsum/7m7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m7y 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]] 1.8Å</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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7m7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m7y OCA], [https://pdbe.org/7m7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m7y RCSB], [https://www.ebi.ac.uk/pdbsum/7m7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m7y ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[https://omim.org/entry/278750 278750]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3'-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3'-OH in the reaction catalyzed by human DNA polymerase (Pol) eta and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3'-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3'-OH using the 2'-OH of a ribonucleotide or 2'-F has little effect on catalysis. Moreover, combining the S113A mutation with 2'-F replacement, which removes two potential hydrogen acceptors of the 3'-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3' via alternative paths, supporting the hypothesis that binding of the third Mg(2+) initiates the reaction by breaking the alpha-beta phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).
		+
		+	Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.,Gregory MT, Gao Y, Cui Q, Yang W Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2103990118. doi: , 10.1073/pnas.2103990118. PMID:34088846<ref>PMID:34088846</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7m7y" 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: Gao Y]]
		+	[[Category: Gregory MT]]
		+	[[Category: Yang W]]

OCA at 14:35, 2 June 2021

OCA — Wed, 02 Jun 2021 14:35:59 GMT

←Older revision		Revision as of 14:35, 2 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7m7y ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7m7y' size='340' side='right'caption='[[7m7y]]' scene=''>
-	~~Authors~~: ~~Gregory, M~~.T.~~, Gao, Y~~.~~, Yang, W~~.	+	== 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~~: ~~Human DNA Pol eta with dA-ended primer and dATP~~: ~~in crystallo reaction for 0 s~~	+	</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=7m7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m7y OCA], [https://pdbe.org/7m7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m7y RCSB], [https://www.ebi.ac.uk/pdbsum/7m7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m7y ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Gao~~, Y]]	+	__TOC__
-	[[Category: ~~Gregory, M.T~~]]	+	</StructureSection>
-	[[Category: ~~Yang, W~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 07:22, 5 May 2021

OCA — Wed, 05 May 2021 07:22:31 GMT

←Older revision		Revision as of 07:22, 5 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7m7y is ON HOLD	+	The entry 7m7y is ON HOLD until Paper Publication

	Authors: Gregory, M.T., Gao, Y., Yang, W.		Authors: Gregory, M.T., Gao, Y., Yang, W.

OCA: Protected "7m7y" [edit=sysop:move=sysop]

OCA — Wed, 07 Apr 2021 04:38:02 GMT

Protected "7m7y" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:38, 7 April 2021

OCA: New page: '''Unreleased structure''' The entry 7m7y is ON HOLD Authors: Gregory, M.T., Gao, Y., Yang, W. Description: Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 0...

OCA — Wed, 07 Apr 2021 04:38:01 GMT

New page: '''Unreleased structure''' The entry 7m7y is ON HOLD Authors: Gregory, M.T., Gao, Y., Yang, W. Description: Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 0...

New page

'''Unreleased structure'''

The entry 7m7y is ON HOLD

Authors: Gregory, M.T., Gao, Y., Yang, W.

Description: Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 0 s
[[Category: Unreleased Structures]]
[[Category: Gao, Y]]
[[Category: Gregory, M.T]]
[[Category: Yang, W]]

7m7y - Revision history

OCA at 16:06, 18 October 2023

OCA at 14:35, 2 June 2021

OCA at 07:22, 5 May 2021

OCA: Protected "7m7y" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7m7y is ON HOLD Authors: Gregory, M.T., Gao, Y., Yang, W. Description: Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 0...