5v1g - Revision history

OCA at 13:39, 4 October 2023

OCA — Wed, 04 Oct 2023 13:39:29 GMT

←Older revision		Revision as of 13:39, 4 October 2023
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	<StructureSection load='5v1g' size='340' side='right'caption='[[5v1g]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5v1g' size='340' side='right'caption='[[5v1g]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v1g]] is a 4 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=5V1G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V1G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v1g]] is a 4 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=5V1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V1G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.798Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</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">[[5vif\|5vif]], [[5vih\|5vih]], [[5vii\|5vii]], [[5vij\|5vij]], [[5vio\|5vio]], [[5vip\|5vip]], [[5vir\|5vir]], [[5vin\|5vin]]</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=5v1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1g OCA], [https://pdbe.org/5v1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v1g RCSB], [https://www.ebi.ac.uk/pdbsum/5v1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1g ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5v1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1g OCA], [~~http~~://pdbe.org/5v1g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v1g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v1g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1g ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>	+	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Freudenthal, B D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Schaich, M A~~]]	+	[[Category: Freudenthal BD]]
-	[[Category: ~~Smith, M R~~]]	+	[[Category: Schaich MA]]
-	[[Category: ~~Whitaker, A M~~]]	+	[[Category: Smith MR]]
-	[[Category: ~~Ligase-dna complex]]~~	+	[[Category: Whitaker AM]]
-	~~[[Category: Transferase ligase / dna]]~~	+
-	~~[[Category: Transferase-dna~~]]	+

OCA at 09:25, 1 January 2020

OCA — Wed, 01 Jan 2020 09:25:55 GMT

←Older revision		Revision as of 09:25, 1 January 2020
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	==DNA polymerase beta binary complex with 8-oxoG at the primer terminus==		==DNA polymerase beta binary complex with 8-oxoG at the primer terminus==
-	<StructureSection load='5v1g' size='340' side='right' caption='[[5v1g]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5v1g' size='340' side='right'caption='[[5v1g]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v1g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V1G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v1g]] is a 4 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=5V1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V1G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vif\|5vif]], [[5vih\|5vih]], [[5vii\|5vii]], [[5vij\|5vij]], [[5vio\|5vio]], [[5vip\|5vip]], [[5vir\|5vir]], [[5vin\|5vin]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vif\|5vif]], [[5vih\|5vih]], [[5vii\|5vii]], [[5vij\|5vij]], [[5vio\|5vio]], [[5vip\|5vip]], [[5vir\|5vir]], [[5vin\|5vin]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5v1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1g OCA], [http://pdbe.org/5v1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1g RCSB], [http://www.ebi.ac.uk/pdbsum/5v1g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1g 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=5v1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1g OCA], [http://pdbe.org/5v1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1g RCSB], [http://www.ebi.ac.uk/pdbsum/5v1g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1g ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5v1g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v1g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Freudenthal, B D]]		[[Category: Freudenthal, B D]]
	[[Category: Schaich, M A]]		[[Category: Schaich, M A]]

OCA at 12:49, 10 May 2017

OCA — Wed, 10 May 2017 12:49:31 GMT

←Older revision		Revision as of 12:49, 10 May 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5v1g is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==DNA polymerase beta binary complex with 8-oxoG at the primer terminus==
		+	<StructureSection load='5v1g' size='340' side='right' caption='[[5v1g]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v1g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V1G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vif\|5vif]], [[5vih\|5vih]], [[5vii\|5vii]], [[5vij\|5vij]], [[5vio\|5vio]], [[5vip\|5vip]], [[5vir\|5vir]], [[5vin\|5vin]]</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=5v1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1g OCA], [http://pdbe.org/5v1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1g RCSB], [http://www.ebi.ac.uk/pdbsum/5v1g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The oxidized nucleotide, 8-oxo-7,8-dihydro-2-deoxyguanosine (8-oxoG), is one of the most abundant DNA lesions. 8-oxoG plays a major role in tumorigenesis and human disease. Biological consequences of 8-oxoG are mediated in part by its insertion into the genome, making it essential to understand how DNA polymerases handle 8-oxoG. Insertion of 8-oxoG is mutagenic when opposite adenine but not when opposite cytosine. However, either result leads to DNA damage at the primer terminus (3-end) during the succeeding insertion event. Extension from DNA damage at primer termini remains poorly understood. Using kinetics and time-lapse crystallography, we evaluated how a model DNA polymerase, human polymerase beta, accommodates 8-oxoG at the primer terminus opposite cytosine and adenine. Notably, extension from the mutagenic base pair is favored over the non-mutagenic base pair. When 8-oxoG is at the primer terminus opposite cytosine, DNA centric changes lead to a clash between O8 of 8-oxoG and the phosphate backbone. Changes in the extension reaction resulting from the altered active site provide evidence for a stabilizing interaction between Arg254 and Asp256 that serves an important role during DNA synthesis reactions. These results provide novel insights into the impact of damage at the primer terminus on genomic stability and DNA synthesis.

-	~~Authors~~:	+	Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.,Whitaker AM, Smith MR, Schaich MA, Freudenthal BD Nucleic Acids Res. 2017 Apr 26. doi: 10.1093/nar/gkx293. PMID:28449123<ref>PMID:28449123</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5v1g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Freudenthal, B D]]
		+	[[Category: Schaich, M A]]
		+	[[Category: Smith, M R]]
		+	[[Category: Whitaker, A M]]
		+	[[Category: Ligase-dna complex]]
		+	[[Category: Transferase ligase / dna]]
		+	[[Category: Transferase-dna]]

OCA at 11:30, 5 April 2017

OCA — Wed, 05 Apr 2017 11:30:00 GMT

←Older revision		Revision as of 11:30, 5 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v1g is ON HOLD	+	The entry 5v1g is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5v1g" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:13:47 GMT

Protected "5v1g" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:13, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5v1g is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 15:13:46 GMT

New page: '''Unreleased structure''' The entry 5v1g is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v1g is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]