6n2s - Revision history

OCA at 06:44, 11 October 2023

2023-10-11T06:44:03Z

←Older revision		Revision as of 06:44, 11 October 2023
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	<StructureSection load='6n2s' size='340' side='right'caption='[[6n2s]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='6n2s' size='340' side='right'caption='[[6n2s]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2s]] 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=6N2S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N2S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=1GC:2-DEOXY-5-O~~-[~~(R)-HYDROXY{~~[~~(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL~~]~~METHYL}PHOSPHORYL~~]~~GUANOSINE'>1GC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.457Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=1CC:5-CARBOXY-2-DEOXYCYTIDINE+MONOPHOSPHATE'>1CC</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1CC:5-CARBOXY-2-DEOXYCYTIDINE+MONOPHOSPHATE'>1CC</scene>, <scene name='pdbligand=1GC:2-DEOXY-5-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]GUANOSINE'>1GC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2s OCA], [https://pdbe.org/6n2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n2s RCSB], [https://www.ebi.ac.uk/pdbsum/6n2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2s 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=6n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2s OCA], [~~http~~://pdbe.org/6n2s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n2s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n2s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2s 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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	</div>		</div>
	<div class="pdbe-citations 6n2s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n2s" 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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Batra~~, V K~~]]	+	[[Category: Batra VK]]
-	[[Category: Wilson~~, S H]]~~	+	[[Category: Wilson SH]]
-	~~[[Category: Conformational change]]~~	+
-	~~[[Category: Dna polymerase beta]]~~	+
-	~~[[Category: Enzyme mechanism]]~~	+
-	~~[[Category: Epigenetic modification]]~~	+
-	~~[[Category: Gene regulation-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:20, 3 April 2019

2019-04-03T08:20:40Z

←Older revision		Revision as of 08:20, 3 April 2019
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	<StructureSection load='6n2s' size='340' side='right'caption='[[6n2s]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='6n2s' size='340' side='right'caption='[[6n2s]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2s]] 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=6N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GC:2-DEOXY-5-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]GUANOSINE'>1GC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GC:2-DEOXY-5-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]GUANOSINE'>1GC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=1CC:5-CARBOXY-2-DEOXYCYTIDINE+MONOPHOSPHATE'>1CC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1CC:5-CARBOXY-2-DEOXYCYTIDINE+MONOPHOSPHATE'>1CC</scene></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=6n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2s OCA], [http://pdbe.org/6n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2s RCSB], [http://www.ebi.ac.uk/pdbsum/6n2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2s 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=6n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2s OCA], [http://pdbe.org/6n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2s RCSB], [http://www.ebi.ac.uk/pdbsum/6n2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2s ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]

OCA at 06:44, 27 March 2019

2019-03-27T06:44:15Z

←Older revision		Revision as of 06:44, 27 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n2s is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position==
		+	<StructureSection load='6n2s' size='340' side='right'caption='[[6n2s]], [[Resolution\|resolution]] 2.46Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n2s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GC:2-DEOXY-5-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]GUANOSINE'>1GC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=1CC:5-CARBOXY-2-DEOXYCYTIDINE+MONOPHOSPHATE'>1CC</scene></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=6n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2s OCA], [http://pdbe.org/6n2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2s RCSB], [http://www.ebi.ac.uk/pdbsum/6n2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2s 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 ==
		+	DNA methylation is an epigenetic mark that regulates gene expression in mammals. One method of methylation removal is through TET-catalyzed oxidation and the base excision repair pathway. The iterative oxidation of 5-methylcytosine (5mC) catalyzed by TET enzymes produces three oxidized forms of cytosine: 5-hydroxmethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC). The effect these modifications have on the efficiency and fidelity of the base excision repair pathway during the repair of opposing base damage, and in particular DNA polymerization, remains to be elucidated. Using kinetic assays, we show that the catalytic efficiency for the incorporation of dGTP catalyzed by human DNA Polymerase beta is not affected when 5mC, 5hmC, 5fC are in the DNA template. In contrast, the catalytic efficiency of dGTP insertion decreases ~20-fold when 5caC is in the templating position, as compared to unmodified cytosine. However, DNA polymerase fidelity is unaltered when these modifications are in the templating position. Structural analysis reveals that the methyl, hydroxymethyl, and formyl modifications are easily accommodated within the polymerase active site. However, to accommodate the carboxy modification, the phosphate backbone on the templating nucleotide shifts ~2.5 A to avoid a potential steric/repulsive clash. This altered conformation is stabilized by lysine 280 which makes a direct interaction with the carboxy modification and the phosphate backbone of the templating strand. This work provides the molecular basis for the accommodation of epigenetic base modifications in a polymerase active site and suggests that these modifications are not mutagenically copied during BER.

-	~~Authors:~~ Batra, V.K.~~, Wilson, S~~.H.	+	Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA Polymerase ss.,Howard MJ, Foley KG, Shock DD, Batra VK, Wilson SH J Biol Chem. 2019 Mar 18. pii: RA118.006809. doi: 10.1074/jbc.RA118.006809. PMID:30885943<ref>PMID:30885943</ref>

-	~~Description: Ternary complex crystal structure~~ of ~~DNA polymerase Beta with 5~~-~~carboxy~~-~~dC (5-caC) at the templating position~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Wilson, S.H]]	+	<div class="pdbe-citations 6n2s" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Batra, V.K~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Batra, V K]]
		+	[[Category: Wilson, S H]]
		+	[[Category: Conformational change]]
		+	[[Category: Dna polymerase beta]]
		+	[[Category: Enzyme mechanism]]
		+	[[Category: Epigenetic modification]]
		+	[[Category: Gene regulation-dna complex]]
		+	[[Category: Transferase-dna complex]]

OCA at 05:14, 5 December 2018

2018-12-05T05:14:49Z

←Older revision		Revision as of 05:14, 5 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n2s is ON HOLD	+	The entry 6n2s is ON HOLD until Paper Publication

	Authors: Batra, V.K., Wilson, S.H.		Authors: Batra, V.K., Wilson, S.H.

OCA: Protected "6n2s" [edit=sysop:move=sysop]

2018-12-02T19:10:34Z

Protected "6n2s" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:10, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n2s is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) ...

2018-12-02T19:10:33Z

New page: '''Unreleased structure''' The entry 6n2s is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) ...

New page

'''Unreleased structure'''

The entry 6n2s is ON HOLD

Authors: Batra, V.K., Wilson, S.H.

Description: Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position
[[Category: Unreleased Structures]]
[[Category: Wilson, S.H]]
[[Category: Batra, V.K]]