6bel - Revision history

OCA at 14:39, 4 October 2023

2023-10-04T14:39:22Z

←Older revision		Revision as of 14:39, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6bel' size='340' side='right'caption='[[6bel]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6bel' size='340' side='right'caption='[[6bel]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bel]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BEL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bel]] 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=6BEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BEL FirstGlance]. <br>
-	</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=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</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]] 1.898Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6bel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bel OCA], [~~http~~://pdbe.org/6bel PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bel RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bel PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bel 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=6bel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bel OCA], [https://pdbe.org/6bel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bel RCSB], [https://www.ebi.ac.uk/pdbsum/6bel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bel 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 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[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: Lfer]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:49, 11 November 2020

2020-11-11T08:49:16Z

←Older revision		Revision as of 08:49, 11 November 2020
Line 1:		Line 1:

	==Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP==		==Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP==
-	<StructureSection load='6bel' size='340' side='right' caption='[[6bel]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6bel' size='340' side='right'caption='[[6bel]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bel]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BEL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bel]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BEL 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=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</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=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</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=6bel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bel OCA], [http://pdbe.org/6bel PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bel RCSB], [http://www.ebi.ac.uk/pdbsum/6bel PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bel ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6bel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bel OCA], [http://pdbe.org/6bel PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bel RCSB], [http://www.ebi.ac.uk/pdbsum/6bel PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bel ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6bel" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bel" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 06:47, 31 October 2018

2018-10-31T06:47:43Z

←Older revision		Revision as of 06:47, 31 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bel is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP==
		+	<StructureSection load='6bel' size='340' side='right' caption='[[6bel]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6bel]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BEL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BEL 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=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</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=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</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=6bel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bel OCA], [http://pdbe.org/6bel PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bel RCSB], [http://www.ebi.ac.uk/pdbsum/6bel PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bel 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 R-isomer~~ of ~~beta-gamma~~-~~CHF~~-~~dCTP~~	+	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 6bel" 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: Transferase-dna complex]]

OCA at 04:56, 20 December 2017

2017-12-20T04:56:36Z

←Older revision		Revision as of 04:56, 20 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

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

2017-11-01T05:00:15Z

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

←Older revision

Revision as of 05:00, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bel is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamm...

2017-11-01T05:00:14Z

New page: '''Unreleased structure''' The entry 6bel is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamm...

New page

'''Unreleased structure'''

The entry 6bel is ON HOLD

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

Description: Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP
[[Category: Unreleased Structures]]
[[Category: Wilson, S.H]]
[[Category: Batra, V.K]]