7u72 - Revision history

OCA at 17:11, 18 October 2023

OCA — Wed, 18 Oct 2023 17:11:54 GMT

←Older revision		Revision as of 17:11, 18 October 2023
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	==Human DNA polymerase eta-DNA ternary mismatch complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion==		==Human DNA polymerase eta-DNA ternary mismatch complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion==
-	<StructureSection load='7u72' size='340' side='right'caption='[[7u72]]' scene=''>	+	<StructureSection load='7u72' size='340' side='right'caption='[[7u72]], [[Resolution\|resolution]] 1.53Å' 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=7U72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U72 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7u72]] is a 3 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=7U72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U72 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=7u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u72 OCA], [https://pdbe.org/7u72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u72 RCSB], [https://www.ebi.ac.uk/pdbsum/7u72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u72 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]] 1.53Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=7u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u72 OCA], [https://pdbe.org/7u72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u72 RCSB], [https://www.ebi.ac.uk/pdbsum/7u72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u72 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 ==
		+	Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase eta. The resulting molecular snapshots suggest primer 3 -OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.
		+
		+	In crystallo observation of three metal ion promoted DNA polymerase misincorporation.,Chang C, Lee Luo C, Gao Y Nat Commun. 2022 Apr 29;13(1):2346. doi: 10.1038/s41467-022-30005-3. PMID:35487947<ref>PMID:35487947</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7u72" 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: Synthetic construct]]
	[[Category: Chang C]]		[[Category: Chang C]]
	[[Category: Gao Y]]		[[Category: Gao Y]]

OCA at 14:52, 31 August 2022

OCA — Wed, 31 Aug 2022 14:52:43 GMT

←Older revision		Revision as of 14:52, 31 August 2022
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-	====	+	==Human DNA polymerase eta-DNA ternary mismatch complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion==
	<StructureSection load='7u72' size='340' side='right'caption='[[7u72]]' scene=''>		<StructureSection load='7u72' size='340' side='right'caption='[[7u72]]' 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'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U72 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=7u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u72 OCA], [https://pdbe.org/7u72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u72 RCSB], [https://www.ebi.ac.uk/pdbsum/7u72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u72 ProSAT]</span></td></tr>		</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=7u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u72 OCA], [https://pdbe.org/7u72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u72 RCSB], [https://www.ebi.ac.uk/pdbsum/7u72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u72 ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Chang C]]
		+	[[Category: Gao Y]]

OCA at 12:53, 4 May 2022

OCA — Wed, 04 May 2022 12:53:19 GMT

←Older revision		Revision as of 12:53, 4 May 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7u72 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7u72' size='340' side='right'caption='[[7u72]]' 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=7u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u72 OCA], [https://pdbe.org/7u72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u72 RCSB], [https://www.ebi.ac.uk/pdbsum/7u72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u72 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 09:30, 30 March 2022

OCA — Wed, 30 Mar 2022 09:30:54 GMT

←Older revision		Revision as of 09:30, 30 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7u72 is ON HOLD	+	The entry 7u72 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7u72" [edit=sysop:move=sysop]

OCA — Wed, 16 Mar 2022 05:03:35 GMT

Protected "7u72" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:03, 16 March 2022

OCA: New page: '''Unreleased structure''' The entry 7u72 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Mar 2022 05:03:34 GMT

New page: '''Unreleased structure''' The entry 7u72 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7u72 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]