6cr3 - Revision history

OCA at 15:09, 4 October 2023

2023-10-04T15:09:57Z

←Older revision		Revision as of 15:09, 4 October 2023
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	==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue==		==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue==
-	<StructureSection load='6cr3' size='340' side='right' caption='[[6cr3]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='6cr3' size='340' side='right'caption='[[6cr3]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cr3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ~~] and [http://en.wikipedia.org/wiki/Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CR3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cr3]] 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=6CR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CR3 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=H84:2-deoxy-5-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine'>H84</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]] 1.95Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=H84:2-deoxy-5-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine'>H84</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=6cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cr3 OCA], [https://pdbe.org/6cr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cr3 RCSB], [https://www.ebi.ac.uk/pdbsum/6cr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cr3 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=6cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cr3 OCA], [~~http~~://pdbe.org/6cr3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cr3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cr3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cr3 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 6cr3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cr3" 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: ~~Batra, V K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Wilson, S H~~]]	+	[[Category: Batra VK]]
-	[[Category: ~~Conformational change]]~~	+	[[Category: Wilson SH]]
-	~~[[Category: Dna polymerase beta]]~~	+
-	~~[[Category: Enzyme mechanism]]~~	+
-	~~[[Category: Lfer]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 06:13, 11 July 2018

2018-07-11T06:13:14Z

←Older revision		Revision as of 06:13, 11 July 2018
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	<StructureSection load='6cr3' size='340' side='right' caption='[[6cr3]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6cr3' size='340' side='right' caption='[[6cr3]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cr3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cr3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CR3 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=H84:2-deoxy-5-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine'>H84</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=H84:2-deoxy-5-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine'>H84</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=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</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=6cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cr3 OCA], [http://pdbe.org/6cr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/6cr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cr3 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=6cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cr3 OCA], [http://pdbe.org/6cr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/6cr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cr3 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 05:36, 27 June 2018

2018-06-27T05:36:51Z

←Older revision		Revision as of 05:36, 27 June 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6cr3 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue==
		+	<StructureSection load='6cr3' size='340' side='right' caption='[[6cr3]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cr3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CR3 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=H84:2-deoxy-5-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine'>H84</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=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</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=6cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cr3 OCA], [http://pdbe.org/6cr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/6cr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cr3 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 ==
		+	We report high-resolution crystal structures of DNA polymerase (pol) beta in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pbeta and Pgamma of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, TTP and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group. Yet, with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important in understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site.

-	~~Authors~~: Batra, V.K., ~~Wilson~~, S.H.	+	Mapping functional substrate-enzyme interactions in the pol beta active site through chemical biology: Structural responses to acidity modification of incoming dNTPs.,Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH Biochemistry. 2018 Jun 6. doi: 10.1021/acs.biochem.8b00418. PMID:29874056<ref>PMID:29874056</ref>

-	~~Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2~~, ~~beta, gamma dATP analogue~~	+	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 6cr3" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Batra, V.K~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Batra, V K]]
		+	[[Category: Wilson, S H]]
		+	[[Category: Conformational change]]
		+	[[Category: Dna polymerase beta]]
		+	[[Category: Enzyme mechanism]]
		+	[[Category: Lfer]]
		+	[[Category: Transcription-dna complex]]

OCA at 03:58, 20 June 2018

2018-06-20T03:58:12Z

←Older revision		Revision as of 03:58, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cr3 is ON HOLD	+	The entry 6cr3 is ON HOLD until Paper Publication

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

OCA: Protected "6cr3" [edit=sysop:move=sysop]

2018-03-28T05:18:10Z

Protected "6cr3" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:18, 28 March 2018

OCA: New page: '''Unreleased structure''' The entry 6cr3 is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated ...

2018-03-28T05:18:09Z

New page: '''Unreleased structure''' The entry 6cr3 is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated ...

New page

'''Unreleased structure'''

The entry 6cr3 is ON HOLD

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

Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue
[[Category: Unreleased Structures]]
[[Category: Wilson, S.H]]
[[Category: Batra, V.K]]