4rpz - Revision history

OCA at 12:54, 1 March 2024

OCA — Fri, 01 Mar 2024 12:54:39 GMT

←Older revision		Revision as of 12:54, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rpz]] 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=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rpz]] 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=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>
-	</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 2.19Å</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [https://pdbe.org/4rpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [https://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz 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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [https://pdbe.org/4rpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [https://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[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>		[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;">
-	== Publication Abstract from PubMed ==
-	One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase beta (hPolbeta). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg2+ appeared during the process of phosphodiester bond formation and was located between the reacting alpha- and beta-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolbeta reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.
-
-	Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.,Vyas R, Reed AJ, Tokarsky EJ, Suo Z J Am Chem Soc. 2015 Apr 9. PMID:25825995<ref>PMID:25825995</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rpz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:23, 8 March 2023

OCA — Wed, 08 Mar 2023 08:23:35 GMT

←Older revision		Revision as of 08:23, 8 March 2023
Line 3:		Line 3:
	<StructureSection load='4rpz' size='340' side='right'caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='4rpz' size='340' side='right'caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rpz]] 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=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rpz]] 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=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>~~</td></tr>~~	+	</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [https://pdbe.org/4rpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [https://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rpx\|4rpx]], [[4rpy\|4rpy]], [[4rq0\|4rq0]], [[4rq1\|4rq1]], [[4rq2\|4rq2]], [[4rq3\|4rq3]], [[4rq4\|4rq4]], [[4rq5\|4rq5]], [[4rq6\|4rq6]], [[4rq7\|4rq7]], [[4rq8\|4rq8]]</td></tr>	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POL B, 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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [~~http~~://pdbe.org/4rpz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz 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 ==
Line 23:		Line 20:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Reed, A J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Suo, Z~~]]	+	[[Category: Reed AJ]]
-	[[Category: ~~Vyas, R~~]]	+	[[Category: Suo Z]]
-	[[Category: ~~Pol beta]]~~	+	[[Category: Vyas R]]
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: X-family~~]]	+

OCA at 10:19, 1 May 2019

OCA — Wed, 01 May 2019 10:19:30 GMT

←Older revision		Revision as of 10:19, 1 May 2019
Line 1:		Line 1:

	==Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s==		==Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s==
-	<StructureSection load='4rpz' size='340' side='right' caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>	+	<StructureSection load='4rpz' size='340' side='right'caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rpz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rpz]] 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=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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">[[4rpx\|4rpx]], [[4rpy\|4rpy]], [[4rq0\|4rq0]], [[4rq1\|4rq1]], [[4rq2\|4rq2]], [[4rq3\|4rq3]], [[4rq4\|4rq4]], [[4rq5\|4rq5]], [[4rq6\|4rq6]], [[4rq7\|4rq7]], [[4rq8\|4rq8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rpx\|4rpx]], [[4rpy\|4rpy]], [[4rq0\|4rq0]], [[4rq1\|4rq1]], [[4rq2\|4rq2]], [[4rq3\|4rq3]], [[4rq4\|4rq4]], [[4rq5\|4rq5]], [[4rq6\|4rq6]], [[4rq7\|4rq7]], [[4rq8\|4rq8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POL B, 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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [http://pdbe.org/4rpz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [http://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz 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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [http://pdbe.org/4rpz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [http://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 4rpz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4rpz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Reed, A J]]		[[Category: Reed, A J]]
	[[Category: Suo, Z]]		[[Category: Suo, Z]]

OCA at 01:50, 10 March 2017

OCA — Fri, 10 Mar 2017 01:50:29 GMT

←Older revision		Revision as of 01:50, 10 March 2017
Line 1:		Line 1:
		+
	==Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s==		==Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s==
	<StructureSection load='4rpz' size='340' side='right' caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='4rpz' size='340' side='right' caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>
Line 6:		Line 7:
	<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">[[4rpx\|4rpx]], [[4rpy\|4rpy]], [[4rq0\|4rq0]], [[4rq1\|4rq1]], [[4rq2\|4rq2]], [[4rq3\|4rq3]], [[4rq4\|4rq4]], [[4rq5\|4rq5]], [[4rq6\|4rq6]], [[4rq7\|4rq7]], [[4rq8\|4rq8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rpx\|4rpx]], [[4rpy\|4rpy]], [[4rq0\|4rq0]], [[4rq1\|4rq1]], [[4rq2\|4rq2]], [[4rq3\|4rq3]], [[4rq4\|4rq4]], [[4rq5\|4rq5]], [[4rq6\|4rq6]], [[4rq7\|4rq7]], [[4rq8\|4rq8]]</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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [http://www.ebi.ac.uk/pdbsum/4rpz 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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [http://pdbe.org/4rpz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [http://www.ebi.ac.uk/pdbsum/4rpz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4rpz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:50, 15 April 2015

OCA — Wed, 15 Apr 2015 12:50:23 GMT

←Older revision		Revision as of 12:50, 15 April 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s==
		+	<StructureSection load='4rpz' size='340' side='right' caption='[[4rpz]], [[Resolution\|resolution]] 2.19Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rpz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RPZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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">[[4rpx\|4rpx]], [[4rpy\|4rpy]], [[4rq0\|4rq0]], [[4rq1\|4rq1]], [[4rq2\|4rq2]], [[4rq3\|4rq3]], [[4rq4\|4rq4]], [[4rq5\|4rq5]], [[4rq6\|4rq6]], [[4rq7\|4rq7]], [[4rq8\|4rq8]]</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=4rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rpz RCSB], [http://www.ebi.ac.uk/pdbsum/4rpz PDBsum]</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 ==
		+	One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase beta (hPolbeta). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg2+ appeared during the process of phosphodiester bond formation and was located between the reacting alpha- and beta-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolbeta reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.

-	~~The entry 4rpz is ON HOLD until Paper Publication~~	+	Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.,Vyas R, Reed AJ, Tokarsky EJ, Suo Z J Am Chem Soc. 2015 Apr 9. PMID:25825995<ref>PMID:25825995</ref>

-	~~Authors: Vyas~~, R.~~, Reed, A~~.~~J., Suo, Z~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Reed, A J]]
	[[Category: Suo, Z]]		[[Category: Suo, Z]]
	[[Category: Vyas, R]]		[[Category: Vyas, R]]
-	[[Category: ~~Reed, A.J~~]]	+	[[Category: Pol beta]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: X-family]]

OCA at 17:12, 24 December 2014

OCA — Wed, 24 Dec 2014 17:12:35 GMT

←Older revision		Revision as of 17:12, 24 December 2014
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	Description: Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s		Description: Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s
		+	[[Category: Unreleased Structures]]
		+	[[Category: Suo, Z]]
		+	[[Category: Vyas, R]]
		+	[[Category: Reed, A.J]]

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

OCA — Wed, 19 Nov 2014 11:29:35 GMT

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

←Older revision

Revision as of 11:29, 19 November 2014

OCA: New page: '''Unreleased structure''' The entry 4rpz is ON HOLD until Paper Publication Authors: Vyas, R., Reed, A.J., Suo, Z. Description: Human DNA Polymerase Beta With Gapped DNA Containing an...

OCA — Wed, 19 Nov 2014 11:29:34 GMT

New page: '''Unreleased structure''' The entry 4rpz is ON HOLD until Paper Publication Authors: Vyas, R., Reed, A.J., Suo, Z. Description: Human DNA Polymerase Beta With Gapped DNA Containing an...

New page

'''Unreleased structure'''

The entry 4rpz is ON HOLD until Paper Publication

Authors: Vyas, R., Reed, A.J., Suo, Z.

Description: Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s