3jpq - Revision history

OCA at 08:00, 6 September 2023

OCA — Wed, 06 Sep 2023 08:00:37 GMT

←Older revision		Revision as of 08:00, 6 September 2023
Line 1:		Line 1:

	==Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate==		==Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate==
-	<StructureSection load='3jpq' size='340' side='right' caption='[[3jpq]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3jpq' size='340' side='right'caption='[[3jpq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jpq]] 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=3JPQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3JPQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jpq]] 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=3JPQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JPQ 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=GBR:5-O-[(R)-{[(S)-[(R)-BROMO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>GBR</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]] 1.9Å</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=GBR:5-O-[(R)-{[(S)-[(R)-BROMO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>GBR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jpn\|3jpn]], [[3jpo\|3jpo]], [[3jpp\|3jpp]], [[3jpr\|3jpr]], [[3jps\|3jps]], [[3jpt\|3jpt]]</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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [https://pdbe.org/3jpq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [https://www.ebi.ac.uk/pdbsum/3jpq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jpq ProSAT]</span></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [~~http~~://pdbe.org/3jpq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3jpq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3jpq 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 31:

	==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: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Batra~~, V K~~]]	+	[[Category: Batra VK]]
-	[[Category: Beard~~, W A~~]]	+	[[Category: Beard WA]]
-	[[Category: Goodman~~, M F~~]]	+	[[Category: Goodman MF]]
-	[[Category: Kashmerov, B]]	+	[[Category: Kashmerov B]]
-	[[Category: McKenna~~, C E~~]]	+	[[Category: McKenna CE]]
-	[[Category: Upton, J]]	+	[[Category: Upton J]]
-	[[Category: Wilson~~, S H]]~~	+	[[Category: Wilson SH]]
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Halogenated analog]]~~	+
-	~~[[Category: Stereoselectivity]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 09:37, 26 December 2018

OCA — Wed, 26 Dec 2018 09:37:29 GMT

←Older revision		Revision as of 09:37, 26 December 2018
Line 17:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/3jpq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/3jpq_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 19:14, 5 August 2016

OCA — Fri, 05 Aug 2016 19:14:55 GMT

←Older revision		Revision as of 19:14, 5 August 2016
Line 1:		Line 1:
		+
	==Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate==		==Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate==
	<StructureSection load='3jpq' size='340' side='right' caption='[[3jpq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3jpq' size='340' side='right' caption='[[3jpq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jpq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JPQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jpq]] 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=3JPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JPQ 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=GBR:5-O-[(R)-{[(S)-[(R)-BROMO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>GBR</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=GBR:5-O-[(R)-{[(S)-[(R)-BROMO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>GBR</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jpn\|3jpn]], [[3jpo\|3jpo]], [[3jpp\|3jpp]], [[3jpr\|3jpr]], [[3jps\|3jps]], [[3jpt\|3jpt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jpn\|3jpn]], [[3jpo\|3jpo]], [[3jpp\|3jpp]], [[3jpr\|3jpr]], [[3jps\|3jps]], [[3jpt\|3jpt]]</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 ~~Homo sapiens~~])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [http://www.ebi.ac.uk/pdbsum/3jpq 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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [http://pdbe.org/3jpq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [http://www.ebi.ac.uk/pdbsum/3jpq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jpq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3jpq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	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 3jpq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Beard, W A]]		[[Category: Beard, W A]]

OCA at 21:14, 25 December 2014

OCA — Thu, 25 Dec 2014 21:14:32 GMT

←Older revision		Revision as of 21:14, 25 December 2014
Line 10:		Line 10:
	<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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [http://www.ebi.ac.uk/pdbsum/3jpq 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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [http://www.ebi.ac.uk/pdbsum/3jpq PDBsum]</span></td></tr>
	</table>		</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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:30, 8 December 2014

OCA — Mon, 08 Dec 2014 09:30:34 GMT

←Older revision		Revision as of 09:30, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3jpq.~~png~~\|~~left~~\|200px]]	+	==Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate==
		+	<StructureSection load='3jpq' size='340' side='right' caption='[[3jpq]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3jpq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JPQ 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=GBR:5-O-[(R)-{[(S)-[(R)-BROMO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>GBR</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jpn\|3jpn]], [[3jpo\|3jpo]], [[3jpp\|3jpp]], [[3jpr\|3jpr]], [[3jps\|3jps]], [[3jpt\|3jpt]]</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 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jpq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jpq RCSB], [http://www.ebi.ac.uk/pdbsum/3jpq PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/3jpq_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta,gamma-Fluoromethylene analogues of nucleotides are considered to be useful mimics of the natural substrates, but direct structural evidence defining their active site interactions has not been available, including the influence of the new chiral center introduced at the CHF carbon, as in beta,gamma-fluoromethylene-dGTP, which forms an active site complex with DNA polymerase beta, a repair enzyme that plays an important role in base excision repair (BER) and oncogenesis. We report X-ray crystallographic results for a series of beta,gamma-CXY dGTP analogues, where X,Y = H, F, Cl, Br, and/or CH(3). For all three R/S monofluorinated analogues examined (CHF, 3/4; CCH(3)F, 13/14; CClF 15/16), a single CXF-diastereomer (3, 13, 16) is observed in the active site complex, with the CXF fluorine atom at a approximately 3 A (bonding) distance to a guanidinium N of Arg183. In contrast, for the CHCl, CHBr, and CHCH(3) analogues, both diasteromers (6/7, 8/9, 10/11) populate the dGTP site in the enzyme complex about equally. The structures of the bound dichloro (5) and dimethyl (12) analogue complexes indicate little to no steric effect on the placement of the bound nucleotide backbone. The results suggest that introduction of a single fluorine atom at the beta,gamma-bridging carbon atom of these dNTP analogues enables a new, stereospecific interaction within the preorganized active site complex that is unique to fluorine. The results also provide the first diverse structural data set permitting an assessment of how closely this class of dNTP analogues mimics the conformation of the parent nucleotide within the active site complex.

-	~~{{STRUCTURE_3jpq\| PDB=3jpq \| SCENE= }}~~	+	Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues.,Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE J Am Chem Soc. 2010 May 13. PMID:20465217<ref>PMID:20465217</ref>

-	~~===Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta~~, ~~gamma-monoBromo methylene triphosphate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20465217}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3jpq]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020465217<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Batra, V K.]]	+	[[Category: Batra, V K]]
-	[[Category: Beard, W A.]]	+	[[Category: Beard, W A]]
-	[[Category: Goodman, M F.]]	+	[[Category: Goodman, M F]]
-	[[Category: Kashmerov, B.]]	+	[[Category: Kashmerov, B]]
-	[[Category: McKenna, C E.]]	+	[[Category: McKenna, C E]]
-	[[Category: Upton, J.]]	+	[[Category: Upton, J]]
-	[[Category: Wilson, S H.]]	+	[[Category: Wilson, S H]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]

OCA at 21:44, 20 October 2012

OCA — Sat, 20 Oct 2012 21:44:13 GMT

←Older revision		Revision as of 21:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3jpq]] is a 4 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA].	+	[[3jpq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA].

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

OCA: Protected "3jpq" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 14:07:55 GMT

Protected "3jpq" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:07, 27 July 2012

OCA at 14:07, 27 July 2012

OCA — Fri, 27 Jul 2012 14:07:52 GMT

←Older revision		Revision as of 14:07, 27 July 2012
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-	{{Seed}}
	[[Image:3jpq.png\|left\|200px]]		[[Image:3jpq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3jpq", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3jpq\| PDB=3jpq \| SCENE= }}		{{STRUCTURE_3jpq\| PDB=3jpq \| SCENE= }}

	===Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate===		===Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20465217}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20465217 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20465217}}		{{ABSTRACT_PUBMED_20465217}}

	==About this Structure==		==About this Structure==
-	~~3JPQ~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA].	+	[[3jpq]] is a 4 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20465217~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020465217</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 44:		Line 35:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:02:22 2010''

OCA at 03:57, 16 June 2010

OCA — Wed, 16 Jun 2010 03:57:41 GMT

←Older revision		Revision as of 03:57, 16 June 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3jpq.~~jpg~~\|left\|200px]]	+	[[Image:3jpq.png\|left\|200px]]

	<!--		<!--
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	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 2 08:33:55 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:02:22 2010''

OCA at 04:29, 2 June 2010

OCA — Wed, 02 Jun 2010 04:29:30 GMT

←Older revision		Revision as of 04:29, 2 June 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3jpq.jpg\|left\|200px]]

-	The ~~entry 3jpq~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3jpq", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3jpq\| PDB=3jpq \| SCENE= }}

-	~~Authors: Batra~~, ~~V.K., Upton, J., Kashmerov, B., Beard, W.A., Wilson, S.H., Goodman, M.F., McKenna, C.E.~~	+	===Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate===

-	Description: Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu May 20 09~~:14:43 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20465217}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20465217 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20465217}}
		+
		+	==About this Structure==
		+	3JPQ is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JPQ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20465217</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Batra, V K.]]
		+	[[Category: Beard, W A.]]
		+	[[Category: Goodman, M F.]]
		+	[[Category: Kashmerov, B.]]
		+	[[Category: McKenna, C E.]]
		+	[[Category: Upton, J.]]
		+	[[Category: Wilson, S H.]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna replication]]
		+	[[Category: Dna synthesis]]
		+	[[Category: Dna-binding]]
		+	[[Category: Dna-directed dna polymerase]]
		+	[[Category: Halogenated analog]]
		+	[[Category: Stereoselectivity]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-dna complex]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 2 08:33:55 2010''