6g2q - Revision history

OCA at 06:18, 11 July 2018

2018-07-11T06:18:07Z

←Older revision		Revision as of 06:18, 11 July 2018
Line 3:		Line 3:
	<StructureSection load='6g2q' size='340' side='right' caption='[[6g2q]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='6g2q' size='340' side='right' caption='[[6g2q]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6g2q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G2Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6g2q]] 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=6G2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G2Q 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=EJH:[(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic+acid'>EJH</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=EJH:[(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic+acid'>EJH</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=6g2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g2q OCA], [http://pdbe.org/6g2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g2q RCSB], [http://www.ebi.ac.uk/pdbsum/6g2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g2q 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=6g2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g2q OCA], [http://pdbe.org/6g2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g2q RCSB], [http://www.ebi.ac.uk/pdbsum/6g2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g2q ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 07:20, 4 July 2018

2018-07-04T07:20:28Z

←Older revision		Revision as of 07:20, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6g2q is ~~ON HOLD~~	+	==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (S-isomer), beta, gamma dTTP analogue==
		+	<StructureSection load='6g2q' size='340' side='right' caption='[[6g2q]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6g2q]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G2Q 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=EJH:[(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic+acid'>EJH</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=6g2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g2q OCA], [http://pdbe.org/6g2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g2q RCSB], [http://www.ebi.ac.uk/pdbsum/6g2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g2q 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 CHCL (~~S-~~isomer), beta, gamma dTTP 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 6g2q" 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: Replication]]

OCA: Protected "6g2q" [edit=sysop:move=sysop]

2018-04-04T04:48:29Z

Protected "6g2q" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:48, 4 April 2018

OCA: New page: '''Unreleased structure''' The entry 6g2q is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated ...

2018-04-04T04:48:27Z

New page: '''Unreleased structure''' The entry 6g2q 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 6g2q 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 CHCL (S-isomer), beta, gamma dTTP analogue
[[Category: Unreleased Structures]]
[[Category: Wilson, S.H]]
[[Category: Batra, V.K]]