4ecz - Revision history

OCA at 08:49, 20 March 2024

2024-03-20T08:49:38Z

←Older revision		Revision as of 08:49, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ecz]] 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=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ecz]] 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=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>
-	</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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]] 1.834Å</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>, <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=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [https://pdbe.org/4ecz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [https://www.ebi.ac.uk/pdbsum/4ecz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ecz ProSAT]</span></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=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [https://pdbe.org/4ecz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [https://www.ebi.ac.uk/pdbsum/4ecz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ecz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== 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>	+	[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 ==		== 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>	+	[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 has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase eta, DNA and dATP were co-crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped by freezing at desired time points for structural analysis. The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.	+

-	Watching DNA polymerase eta make a phosphodiester bond.,Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W Nature. 2012 Jul 11;487(7406):196-201. doi: 10.1038/nature11181. PMID:22785315<ref>PMID:22785315</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 4ecz" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:05, 28 September 2022

2022-09-28T07:05:14Z

←Older revision		Revision as of 07:05, 28 September 2022
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	==Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion==		==Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion==
-	<StructureSection load='4ecz' size='340' side='right' caption='[[4ecz]], [[Resolution\|resolution]] 1.83Å' scene=''>	+	<StructureSection load='4ecz' size='340' side='right'caption='[[4ecz]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ecz]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ecz]] 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=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene~~></td></tr>~~	+	</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ecq\|4ecq]], [[4ecr\|4ecr]], [[4ecs\|4ecs]], [[4ect\|4ect]], [[4ecu\|4ecu]], [[4ecv\|4ecv]], [[4ecw\|4ecw]], [[4ecx\|4ecx]], [[4ecy\|4ecy]], [[4ed0\|4ed0]], [[4ed1\|4ed1]], [[4ed2\|4ed2]], [[4ed3\|4ed3]], [[4ed6\|4ed6]], [[4ed7\|4ed7]], [[4ed8\|4ed8]]</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=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [https://pdbe.org/4ecz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [https://www.ebi.ac.uk/pdbsum/4ecz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ecz ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [~~http~~://pdbe.org/4ecz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ecz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ecz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[~~http~~://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>	+	[[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 ==		== Function ==
-	[[~~http~~://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>	+	[[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4ecz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ecz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Nakamura, T]]	+	[[Category: Nakamura T]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	[[Category: Zhao, Y]]	+	[[Category: Zhao Y]]
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 13:20, 4 August 2016

2016-08-04T13:20:33Z

←Older revision		Revision as of 13:20, 4 August 2016
Line 1:		Line 1:
		+
	==Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion==		==Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion==
	<StructureSection load='4ecz' size='340' side='right' caption='[[4ecz]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='4ecz' size='340' side='right' caption='[[4ecz]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ecq\|4ecq]], [[4ecr\|4ecr]], [[4ecs\|4ecs]], [[4ect\|4ect]], [[4ecu\|4ecu]], [[4ecv\|4ecv]], [[4ecw\|4ecw]], [[4ecx\|4ecx]], [[4ecy\|4ecy]], [[4ed0\|4ed0]], [[4ed1\|4ed1]], [[4ed2\|4ed2]], [[4ed3\|4ed3]], [[4ed6\|4ed6]], [[4ed7\|4ed7]], [[4ed8\|4ed8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ecq\|4ecq]], [[4ecr\|4ecr]], [[4ecs\|4ecs]], [[4ect\|4ect]], [[4ecu\|4ecu]], [[4ecv\|4ecv]], [[4ecw\|4ecw]], [[4ecx\|4ecx]], [[4ecy\|4ecy]], [[4ed0\|4ed0]], [[4ed1\|4ed1]], [[4ed2\|4ed2]], [[4ed3\|4ed3]], [[4ed6\|4ed6]], [[4ed7\|4ed7]], [[4ed8\|4ed8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [http://www.ebi.ac.uk/pdbsum/4ecz PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [http://pdbe.org/4ecz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [http://www.ebi.ac.uk/pdbsum/4ecz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ecz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ecz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Nakamura, T]]		[[Category: Nakamura, T]]
	[[Category: Yang, W]]		[[Category: Yang, W]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 10:41, 21 December 2014

2014-12-21T10:41:45Z

←Older revision		Revision as of 10:41, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ecz\| PDB=4ecz \| SCENE= }}~~	+	==Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion==
-	===Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion===	+	<StructureSection load='4ecz' size='340' side='right' caption='[[4ecz]], [[Resolution\|resolution]] 1.83Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22785315}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ECZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ecq\|4ecq]], [[4ecr\|4ecr]], [[4ecs\|4ecs]], [[4ect\|4ect]], [[4ecu\|4ecu]], [[4ecv\|4ecv]], [[4ecw\|4ecw]], [[4ecx\|4ecx]], [[4ecy\|4ecy]], [[4ed0\|4ed0]], [[4ed1\|4ed1]], [[4ed2\|4ed2]], [[4ed3\|4ed3]], [[4ed6\|4ed6]], [[4ed7\|4ed7]], [[4ed8\|4ed8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ecz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ecz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ecz RCSB], [http://www.ebi.ac.uk/pdbsum/4ecz PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[http://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 ==
		+	[[http://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 has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase eta, DNA and dATP were co-crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped by freezing at desired time points for structural analysis. The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.

-	~~==Disease==~~	+	Watching DNA polymerase eta make a phosphodiester bond.,Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W Nature. 2012 Jul 11;487(7406):196-201. doi: 10.1038/nature11181. PMID:22785315<ref>PMID:22785315</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type~~ (~~XPV~~) ~~[MIM~~:~~[http~~:~~//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==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/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>
-		+
-	~~==About this Structure==~~	+
-	[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA].	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:022785315</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Nakamura, T.]]	+	[[Category: Nakamura, T]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
-	[[Category: Zhao, Y.]]	+	[[Category: Zhao, Y]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 19:18, 24 March 2013

2013-03-24T19:18:24Z

←Older revision		Revision as of 19:18, 24 March 2013
Line 1:		Line 1:
-	[[Image:4ecz.png\|left\|200px]]
-
	{{STRUCTURE_4ecz\| PDB=4ecz \| SCENE= }}		{{STRUCTURE_4ecz\| PDB=4ecz \| SCENE= }}
-
	===Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion===		===Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion===
-
	{{ABSTRACT_PUBMED_22785315}}		{{ABSTRACT_PUBMED_22785315}}
		+
		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[http://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==
		+	[[http://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>

	==About this Structure==		==About this Structure==
	[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA].		[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022785315</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022785315</ref><references group="xtra"/><references/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 06:01, 25 July 2012

2012-07-25T06:01:32Z

←Older revision		Revision as of 06:01, 25 July 2012
Line 1:		Line 1:
-	[[Image:4ecz.~~jpg~~\|left\|200px]]	+	[[Image:4ecz.png\|left\|200px]]

	{{STRUCTURE_4ecz\| PDB=4ecz \| SCENE= }}		{{STRUCTURE_4ecz\| PDB=4ecz \| SCENE= }}
Line 5:		Line 5:
	===Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion===		===Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion===

		+	{{ABSTRACT_PUBMED_22785315}}

	==About this Structure==		==About this Structure==
	[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA].		[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022785315</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 08:24, 11 July 2012

2012-07-11T08:24:04Z

←Older revision		Revision as of 08:24, 11 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4ecz.jpg\|left\|200px]]

-	~~The entry~~ 4ecz ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4ecz\| PDB=4ecz \| SCENE= }}

-	~~Authors~~: ~~Nakamura, T., Zhao, Y., Yang, W~~.	+	===Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion===

-	~~Description~~: ~~Human~~ DNA ~~polymerase eta~~ -DNA ~~ternary complex~~: ~~AT crystal at pH 6~~.~~5 (Na+ MES) with 1 Ca2+ ion~~	+
		+	==About this Structure==
		+	[[4ecz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ECZ OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Nakamura, T.]]
		+	[[Category: Yang, W.]]
		+	[[Category: Zhao, Y.]]
		+	[[Category: Transferase-dna complex]]

OCA at 18:54, 2 May 2012

2012-05-02T18:54:12Z

←Older revision		Revision as of 18:54, 2 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ecz is ON HOLD	+	The entry 4ecz is ON HOLD until Paper Publication

	Authors: Nakamura, T., Zhao, Y., Yang, W.		Authors: Nakamura, T., Zhao, Y., Yang, W.

-	Description: Human DNA polymerase eta --DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion	+	Description: Human DNA polymerase eta -DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion

OCA: Protected "4ecz" [edit=sysop:move=sysop]

2012-04-04T05:48:52Z

Protected "4ecz" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:48, 4 April 2012

OCA: New page: '''Unreleased structure''' The entry 4ecz is ON HOLD Authors: Nakamura, T., Zhao, Y., Yang, W. Description: Human DNA polymerase eta --DNA ternary complex: AT crystal at pH 6.5 (Na+ ME...

2012-04-04T05:48:52Z

New page: '''Unreleased structure''' The entry 4ecz is ON HOLD Authors: Nakamura, T., Zhao, Y., Yang, W. Description: Human DNA polymerase eta --DNA ternary complex: AT crystal at pH 6.5 (Na+ ME...

New page

'''Unreleased structure'''

The entry 4ecz is ON HOLD

Authors: Nakamura, T., Zhao, Y., Yang, W.

Description: Human DNA polymerase eta --DNA ternary complex: AT crystal at pH 6.5 (Na+ MES) with 1 Ca2+ ion