5dga - Revision history

OCA at 08:46, 27 September 2023

2023-09-27T08:46:42Z

←Older revision		Revision as of 08:46, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DGA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DGA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</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">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [https://pdbe.org/5dga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [https://www.ebi.ac.uk/pdbsum/5dga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga 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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [https://pdbe.org/5dga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [https://www.ebi.ac.uk/pdbsum/5dga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:34, 21 June 2023

2023-06-21T10:34:20Z

←Older revision		Revision as of 10:34, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5dga' size='340' side='right'caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5dga' size='340' side='right'caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DGA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</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=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [https://pdbe.org/5dga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [https://www.ebi.ac.uk/pdbsum/5dga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dg7\|5dg7]]~~, ~~[[5dg8\|5dg8]], [[5dg9\|5dg9]], [[5dgb\|5dgb]]~~<~~/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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [~~http~~://pdbe.org/5dga PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dga PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga 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 31:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Egli, M~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Patra, A~~]]	+	[[Category: Egli M]]
-	[[Category: ~~Dna damage]]~~	+	[[Category: Patra A]]
-	~~[[Category: Dna enzyme]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Etheno dna adduct]]~~	+
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: Translesion dna synthesis~~]]	+

OCA at 08:58, 4 December 2019

2019-12-04T08:58:20Z

←Older revision		Revision as of 08:58, 4 December 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dT PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA==		==CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dT PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA==
-	<StructureSection load='5dga' size='340' side='right' caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5dga' size='340' side='right'caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGA FirstGlance]. <br>
Line 24:		Line 24:
	</div>		</div>
	<div class="pdbe-citations 5dga" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dga" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 33:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Patra, A]]		[[Category: Patra, A]]

OCA at 12:32, 6 November 2017

2017-11-06T12:32:37Z

←Older revision		Revision as of 12:32, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5dga' size='340' side='right' caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5dga' size='340' side='right' caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dga]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dga]] 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=5DGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</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=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dg7\|5dg7]], [[5dg8\|5dg8]], [[5dg9\|5dg9]], [[5dgb\|5dgb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dg7\|5dg7]], [[5dg8\|5dg8]], [[5dg9\|5dg9]], [[5dgb\|5dgb]]</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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [http://pdbe.org/5dga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [http://www.ebi.ac.uk/pdbsum/5dga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga ProSAT]</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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [http://pdbe.org/5dga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [http://www.ebi.ac.uk/pdbsum/5dga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga ProSAT]</span></td></tr>
Line 28:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Patra, A]]		[[Category: Patra, A]]

OCA at 03:09, 13 July 2016

2016-07-13T03:09:55Z

←Older revision		Revision as of 03:09, 13 July 2016
Line 8:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dg7\|5dg7]], [[5dg8\|5dg8]], [[5dg9\|5dg9]], [[5dgb\|5dgb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dg7\|5dg7]], [[5dg8\|5dg8]], [[5dg9\|5dg9]], [[5dgb\|5dgb]]</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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [http://pdbe.org/5dga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [http://www.ebi.ac.uk/pdbsum/5dga 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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [http://pdbe.org/5dga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [http://www.ebi.ac.uk/pdbsum/5dga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dga ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 07:48, 20 June 2016

2016-06-20T07:48:07Z

←Older revision		Revision as of 07:48, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dga is ~~ON HOLD~~ until ~~Paper~~ Publication	+	==CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dT PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA==
		+	<StructureSection load='5dga' size='340' side='right' caption='[[5dga]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dga]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DGA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1FZ:5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE'>1FZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDA:3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5-MONOPHOSPHATE'>EDA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dg7\|5dg7]], [[5dg8\|5dg8]], [[5dg9\|5dg9]], [[5dgb\|5dgb]]</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=5dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dga OCA], [http://pdbe.org/5dga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dga RCSB], [http://www.ebi.ac.uk/pdbsum/5dga 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 ==
		+	1,N6-Ethenodeoxyadenosine (1,N6-epsilondA) is the major etheno lesion formed in the reaction of DNA with epoxides substituted with good leaving groups (e.g., vinyl chloride epoxide). This lesion is also formed endogenously in DNA from lipid oxidation. Recombinant human DNA polymerase eta (hpol eta) can replicate oligonucleotide templates containing 1,N6-epsilondA. In steady-state kinetic analysis, hpol eta preferred to incorporate dATP and dGTP, compared to dTTP. Mass spectral analysis of incorporation products also showed preferred purine (A, G) incorporation and extensive -1 frameshifts, suggesting pairing of the inserted purine and slippage before further replication. Five X-ray crystal structures of hpol eta ternary complexes were determined, three at the insertion and two at the extension stage. Two insertion complexes revealed incoming non-hydrolyzable dATP or dGTP analogs not pairing with but instead in a staggered configuration relative to 1,N6-epsilondA in the anti conformation, thus opposite the 5 prime-T in the template, explaining the proclivity for frameshift misincorporation. In another insertion complex, dTTP was positioned opposite 1,N6-epsilondA and the adduct base was in the syn conformation, with formation of two hydrogen bonds. At the extension stage, with either an incorporated dA or dT opposite 1,N6-epsilondA and dTMPNPP opposite the 5 prime-A, the 3 prime-terminal nucleoside of the primer was disordered, consistent with the tendency not to incorporate dTTP opposite 1,N6-epsilondA. Collectively the results show a preference for purine pairing opposite 1,N6-epsilondA and for -1 frameshifts.

-	~~Authors: Patra~~, A., ~~Egli~~, M.	+	Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta.,Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M J Biol Chem. 2016 May 16. pii: jbc.M116.732487. PMID:27226627<ref>PMID:27226627</ref>

-	~~Description: CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1~~,N6-~~ETHENODEOXYADENOSINE~~ : ~~dT PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5dga" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Patra, A]]		[[Category: Patra, A]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna enzyme]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Etheno dna adduct]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: Translesion dna synthesis]]

OCA at 12:58, 30 September 2015

2015-09-30T12:58:25Z

←Older revision		Revision as of 12:58, 30 September 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dga is ON HOLD	+	The entry 5dga is ON HOLD until Paper Publication

	Authors: Patra, A., Egli, M.		Authors: Patra, A., Egli, M.

OCA: Protected "5dga" [edit=sysop:move=sysop]

2015-09-02T11:37:44Z

Protected "5dga" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:37, 2 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dga is ON HOLD Authors: Patra, A., Egli, M. Description: CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dT...

2015-09-02T11:37:43Z

New page: '''Unreleased structure''' The entry 5dga is ON HOLD Authors: Patra, A., Egli, M. Description: CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dT...

New page

'''Unreleased structure'''

The entry 5dga is ON HOLD

Authors: Patra, A., Egli, M.

Description: CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dT PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA
[[Category: Unreleased Structures]]
[[Category: Egli, M]]
[[Category: Patra, A]]