3jaa - Revision history

OCA at 08:42, 7 February 2024

2024-02-07T08:42:02Z

←Older revision		Revision as of 08:42, 7 February 2024
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	<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>		<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jaa]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 22Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ja9\|3ja9]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([https://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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [https://pdbe.org/3jaa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [https://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa 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=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [https://pdbe.org/3jaa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [https://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa 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 ==~~	+
-	Translesion synthesis (TLS) is the mechanism by which DNA polymerases replicate through unrepaired DNA lesions. TLS is activated by monoubiquitination of the homotrimeric proliferating cell nuclear antigen (PCNA) at lysine-164, followed by the switch from replicative to specialized polymerases at DNA damage sites. Pol eta belongs to the Y-Family of specialized polymerases that can efficiently bypass UV-induced lesions. Like other members of the Y-Family polymerases, its recruitment to the damaged sites is mediated by the interaction with monoubiquitinated PCNA (Ub-PCNA) via its ubiquitin-binding domain and non-canonical PCNA-interacting motif in the C-terminal region. The structural determinants underlying the direct recognition of Ub-PCNA by Pol eta, or Y-Family polymerases in general, remain largely unknown. Here we report a structure of the Ub-PCNA/Pol eta complex bound to DNA determined by single-particle electron microscopy (EM). The overall obtained structure resembles that of the editing PCNA/PolB complex. Analysis of the map revealed the conformation of ubiquitin that binds the C-terminal domain of Pol eta. Our present study suggests that the Ub-PCNA/Pol eta interaction requires the formation of a structured binding interface, which is dictated by the inherent flexibility of Ub-PCNA.	+

-	~~Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA.,Lau WC, Li Y, Zhang Q, Huen MS Sci Rep. 2015 Oct 27;5:15759. doi: 10.1038/srep15759. PMID:26503230<ref>PMID:26503230</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 3jaa" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huen, M S.Y~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Lau, W C.Y~~]]	+	[[Category: Huen MSY]]
-	[[Category: ~~Li, Y~~]]	+	[[Category: Lau WCY]]
-	[[Category: ~~Zhang, Q~~]]	+	[[Category: Li Y]]
-	[[Category: ~~Cpd]]~~	+	[[Category: Zhang Q]]
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Pol eta]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Thymine dimer]]~~	+
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: Xeroderma pigm variant]]~~	+
-	~~[[Category: Xpv~~]]	+

OCA at 13:29, 4 May 2022

2022-05-04T13:29:36Z

OCA at 18:18, 10 April 2020

2020-04-10T18:18:55Z

←Older revision		Revision as of 18:18, 10 April 2020
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	<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>		<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3JAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ja9\|3ja9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ja9\|3ja9]]</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='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=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [http://pdbe.org/3jaa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [http://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [http://pdbe.org/3jaa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [http://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 17:34, 6 March 2020

2020-03-06T17:34:18Z

←Older revision		Revision as of 17:34, 6 March 2020
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	==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==		==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==
-	<~~StructureSection~~ load='3jaa' size='340' side='right'caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>	+	<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
Line 26:		Line 26:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]

OCA at 07:18, 23 October 2019

2019-10-23T07:18:23Z

←Older revision		Revision as of 07:18, 23 October 2019
Line 1:		Line 1:

	==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==		==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==
-	<StructureSection load='3jaa' size='340' side='right' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>	+	<StructureSection load='3jaa' size='340' side='right'caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
Line 29:		Line 29:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Huen, M S.Y]]		[[Category: Huen, M S.Y]]
	[[Category: Lau, W C.Y]]		[[Category: Lau, W C.Y]]

OCA at 09:54, 19 December 2018

2018-12-19T09:54:27Z

←Older revision		Revision as of 09:54, 19 December 2018
Line 1:		Line 1:
		+
	==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==		==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==
	<StructureSection load='3jaa' size='340' side='right' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>		<StructureSection load='3jaa' size='340' side='right' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jaa]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ja9\|3ja9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ja9\|3ja9]]</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=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [http://pdbe.org/3jaa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [http://www.ebi.ac.uk/pdbsum/3jaa 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=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [http://pdbe.org/3jaa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [http://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 26:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
	[[Category: Huen, M S.Y]]		[[Category: Huen, M S.Y]]
	[[Category: Lau, W C.Y]]		[[Category: Lau, W C.Y]]

OCA at 12:41, 23 December 2015

2015-12-23T12:41:13Z

←Older revision		Revision as of 12:41, 23 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)==
		+	<StructureSection load='3jaa' size='340' side='right' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3jaa]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ja9\|3ja9]]</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=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [http://pdbe.org/3jaa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [http://www.ebi.ac.uk/pdbsum/3jaa 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 ==
		+	Translesion synthesis (TLS) is the mechanism by which DNA polymerases replicate through unrepaired DNA lesions. TLS is activated by monoubiquitination of the homotrimeric proliferating cell nuclear antigen (PCNA) at lysine-164, followed by the switch from replicative to specialized polymerases at DNA damage sites. Pol eta belongs to the Y-Family of specialized polymerases that can efficiently bypass UV-induced lesions. Like other members of the Y-Family polymerases, its recruitment to the damaged sites is mediated by the interaction with monoubiquitinated PCNA (Ub-PCNA) via its ubiquitin-binding domain and non-canonical PCNA-interacting motif in the C-terminal region. The structural determinants underlying the direct recognition of Ub-PCNA by Pol eta, or Y-Family polymerases in general, remain largely unknown. Here we report a structure of the Ub-PCNA/Pol eta complex bound to DNA determined by single-particle electron microscopy (EM). The overall obtained structure resembles that of the editing PCNA/PolB complex. Analysis of the map revealed the conformation of ubiquitin that binds the C-terminal domain of Pol eta. Our present study suggests that the Ub-PCNA/Pol eta interaction requires the formation of a structured binding interface, which is dictated by the inherent flexibility of Ub-PCNA.

-	~~The entry 3jaa is ON HOLD~~	+	Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA.,Lau WC, Li Y, Zhang Q, Huen MS Sci Rep. 2015 Oct 27;5:15759. doi: 10.1038/srep15759. PMID:26503230<ref>PMID:26503230</ref>

-	~~Authors: Lau~~, ~~W.C.Y., Li, Y., Zhang, Q., Huen, M~~.S.Y.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~HUMAN~~ DNA ~~POLYMERASE ETA in COMPLEX WITH NORMAL~~ DNA ~~AND INCO NUCLEOTIDE (NRM)~~	+	<div class="pdbe-citations 3jaa" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Huen, M S.Y]]
		+	[[Category: Lau, W C.Y]]
	[[Category: Li, Y]]		[[Category: Li, Y]]
-	[[Category: Huen, M.S.Y]]
-	[[Category: Lau, W.C.Y]]
	[[Category: Zhang, Q]]		[[Category: Zhang, Q]]
		+	[[Category: Cpd]]
		+	[[Category: Dna damage]]
		+	[[Category: Pol eta]]
		+	[[Category: Polymerase]]
		+	[[Category: Thymine dimer]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: Xeroderma pigm variant]]
		+	[[Category: Xpv]]

OCA at 07:24, 24 June 2015

2015-06-24T07:24:09Z

←Older revision		Revision as of 07:24, 24 June 2015
Line 3:		Line 3:
	The entry 3jaa is ON HOLD		The entry 3jaa is ON HOLD

-	Authors: ,, ,, ,, ,	+	Authors: Lau, W.C.Y., Li, Y., Zhang, Q., Huen, M.S.Y.

-	Description: HUMAN DNA POLYMERASE ETA IN COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)	+	Description: HUMAN DNA POLYMERASE ETA in COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ,, ,, ~~,, ,~~]]	+	[[Category: Li, Y]]
		+	[[Category: Huen, M.S.Y]]
		+	[[Category: Lau, W.C.Y]]
		+	[[Category: Zhang, Q]]

OCA: Protected "3jaa" [edit=sysop:move=sysop]

2015-05-27T10:41:52Z

Protected "3jaa" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:41, 27 May 2015

OCA: New page: '''Unreleased structure''' The entry 3jaa is ON HOLD Authors: ,, ,, ,, , Description: HUMAN DNA POLYMERASE ETA IN COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM) [[Category: Unreleas...

2015-05-27T10:41:50Z

New page: '''Unreleased structure''' The entry 3jaa is ON HOLD Authors: ,, ,, ,, , Description: HUMAN DNA POLYMERASE ETA IN COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM) [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 3jaa is ON HOLD

Authors: ,, ,, ,, ,

Description: HUMAN DNA POLYMERASE ETA IN COMPLEX WITH NORMAL DNA AND INCO NUCLEOTIDE (NRM)
[[Category: Unreleased Structures]]
[[Category: ,, ,, ,, ,]]

←Older revision		Revision as of 13:29, 4 May 2022
Line 3:		Line 3:
	<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>		<SX load='3jaa' size='340' side='right' viewer='molstar' caption='[[3jaa]], [[Resolution\|resolution]] 22.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jaa]] 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=3JAA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3JAA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jaa]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JAA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DZ4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>DZ4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ja9\|3ja9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ja9\|3ja9]]</div></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLH, RAD30, RAD30A, XPV ([https://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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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~~://proteopedia.org/fgij/fg.htm?mol=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [~~http~~://pdbe.org/3jaa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa 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=3jaa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jaa OCA], [https://pdbe.org/3jaa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jaa RCSB], [https://www.ebi.ac.uk/pdbsum/3jaa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jaa 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 ==