3nae - Revision history

OCA at 09:12, 6 September 2023

OCA — Wed, 06 Sep 2023 09:12:03 GMT

←Older revision		Revision as of 09:12, 6 September 2023
Line 1:		Line 1:

	==RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin==		==RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin==
-	<StructureSection load='3nae' size='340' side='right' caption='[[3nae]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3nae' size='340' side='right'caption='[[3nae]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nae]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpr69 Bpr69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NAE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nae]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NAE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=DTP:~~2~~-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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]] 2.003Å</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>, <scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l8b\|3l8b]], [[3lzi\|3lzi]], [[3lzj\|3lzj]], [[2ozs\|2ozs]], [[1ig9\|1ig9]]</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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [https://pdbe.org/3nae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [https://www.ebi.ac.uk/pdbsum/3nae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nae ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [~~http~~://pdbe.org/3nae PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nae PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nae ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.	+	[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	== 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: ~~Bpr69~~]]	+	[[Category: Escherichia phage RB69]]
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Large Structures]]
-	[[Category: Beckman, J]]	+	[[Category: Beckman J]]
-	[[Category: Blaha, G]]	+	[[Category: Blaha G]]
-	[[Category: Konigsberg~~, W H~~]]	+	[[Category: Konigsberg WH]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	[[Category: Wang, M]]	+	[[Category: Wang M]]
-	~~[[Category: Fidelity]]~~	+
-	~~[[Category: Guanidinohydantoin]]~~	+
-	~~[[Category: Rb69 dna polymerase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 13:46, 16 January 2019

OCA — Wed, 16 Jan 2019 13:46:18 GMT

←Older revision		Revision as of 13:46, 16 January 2019
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/na/3nae_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/na/3nae_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 23:50, 4 August 2016

OCA — Thu, 04 Aug 2016 23:50:38 GMT

←Older revision		Revision as of 23:50, 4 August 2016
Line 1:		Line 1:
		+
	==RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin==		==RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin==
	<StructureSection load='3nae' size='340' side='right' caption='[[3nae]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3nae' size='340' side='right' caption='[[3nae]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_rb69 Enterobacteria phage rb69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NAE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NAE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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>, <scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</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>, <scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l8b\|3l8b]], [[3lzi\|3lzi]], [[3lzj\|3lzj]], [[2ozs\|2ozs]], [[1ig9\|1ig9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l8b\|3l8b]], [[3lzi\|3lzi]], [[3lzj\|3lzj]], [[2ozs\|2ozs]], [[1ig9\|1ig9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 ~~Enterobacteria phage RB69~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [http://www.ebi.ac.uk/pdbsum/3nae 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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [http://pdbe.org/3nae PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [http://www.ebi.ac.uk/pdbsum/3nae PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nae 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=3nae 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 3nae" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Enterobacteria phage rb69]]
	[[Category: Beckman, J]]		[[Category: Beckman, J]]
	[[Category: Blaha, G]]		[[Category: Blaha, G]]

OCA at 20:53, 24 December 2014

OCA — Wed, 24 Dec 2014 20:53:01 GMT

←Older revision		Revision as of 20:53, 24 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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [http://www.ebi.ac.uk/pdbsum/3nae 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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [http://www.ebi.ac.uk/pdbsum/3nae PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:05, 9 December 2014

OCA — Tue, 09 Dec 2014 10:05:33 GMT

←Older revision		Revision as of 10:05, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3nae.~~png~~\|~~left~~\|200px]]	+	==RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin==
		+	<StructureSection load='3nae' size='340' side='right' caption='[[3nae]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NAE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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>, <scene name='pdbligand=G35:(5R)-5-CARBAMIMIDAMIDO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)IMIDAZOLIDINE-2,4-DIONE'>G35</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l8b\|3l8b]], [[3lzi\|3lzi]], [[3lzj\|3lzj]], [[2ozs\|2ozs]], [[1ig9\|1ig9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])</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=3nae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nae OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nae RCSB], [http://www.ebi.ac.uk/pdbsum/3nae 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/na/3nae_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 ==
		+	Continuous oxidative damage inflicted on DNA produces 7,8-dihydro-8-oxoguanine (8-oxoG), a commonly occurring lesion that can potentially cause cancer by producing G --> T transversions during DNA replication. Mild oxidation of 8-oxoG leads to the formation of hydantoins, specifically guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), which are 100% mutagenic because they encode almost exclusively the insertion of dAMP and dGMP (encoding G --> T and G --> C transversions, respectively). The wild-type (wt) pol alpha family DNA polymerase from bacteriophage RB69 (RB69pol) inserts dAMP and dGMP with low efficiency when situated opposite Gh. In contrast, the RB69pol Y567A mutant inserts both of these dNMPs opposite Gh with >100-fold higher efficiency than wt. We now report the crystal structure of the "closed" preinsertion complex for the Y567A mutant with dATP opposite a templating Gh (R-configuration) in a 13/18mer primer-template (P/T) at 2.0 A resolution. The structure data reveal that the Y to A substitution provides the nascent base pair binding pocket (NBP) with the flexibility to accommodate Gh by allowing G568 to move in the major-to-minor groove direction of the P/T. Thus, Gh is rejected as a templating base by wt RB69pol because G568 is inflexible, preventing Gh from pairing with the incoming dATP or dGTP base.

-	~~{{STRUCTURE_3nae\| PDB=3nae \| SCENE= }}~~	+	Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP and dGMP To Be Inserted opposite Guanidinohydantoin .,Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH Biochemistry. 2010 Sep 9. PMID:20795733<ref>PMID:20795733</ref>

-	~~===RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20795733}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3nae]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020795733<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]
-	[[Category: Beckman, J.]]	+	[[Category: Beckman, J]]
-	[[Category: Blaha, G.]]	+	[[Category: Blaha, G]]
-	[[Category: Konigsberg, W H.]]	+	[[Category: Konigsberg, W H]]
-	[[Category: Wang, J.]]	+	[[Category: Wang, J]]
-	[[Category: Wang, M.]]	+	[[Category: Wang, M]]
	[[Category: Fidelity]]		[[Category: Fidelity]]
	[[Category: Guanidinohydantoin]]		[[Category: Guanidinohydantoin]]
	[[Category: Rb69 dna polymerase]]		[[Category: Rb69 dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 09:01, 20 October 2012

OCA — Sat, 20 Oct 2012 09:01:59 GMT

←Older revision		Revision as of 09:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3nae]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].	+	[[3nae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].

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

OCA at 21:34, 25 July 2012

OCA — Wed, 25 Jul 2012 21:34:15 GMT

←Older revision		Revision as of 21:34, 25 July 2012
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	[[Image:3nae.png\|left\|200px]]		[[Image:3nae.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3nae", 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_3nae\| PDB=3nae \| SCENE= }}		{{STRUCTURE_3nae\| PDB=3nae \| SCENE= }}

	===RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin===		===RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20795733}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20795733 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20795733}}		{{ABSTRACT_PUBMED_20795733}}

	==About this Structure==		==About this Structure==
-	[[3nae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].	+	[[3nae]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20795733~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020795733</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]

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

OCA — Wed, 29 Dec 2010 17:59:15 GMT

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

←Older revision

Revision as of 17:59, 29 December 2010

OCA at 17:59, 29 December 2010

OCA — Wed, 29 Dec 2010 17:59:13 GMT

←Older revision		Revision as of 17:59, 29 December 2010
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-	~~{{Seed}}~~	+	[[Image:3nae.png\|left\|200px]]
-	[[Image:3nae.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	~~3NAE~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].	+	[[3nae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].

	==Reference==		==Reference==
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	[[Category: Rb69 dna polymerase]]		[[Category: Rb69 dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 15 10:50:59 2010''

OCA at 07:42, 15 September 2010

OCA — Wed, 15 Sep 2010 07:42:18 GMT

←Older revision		Revision as of 07:42, 15 September 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3nae.jpg\|left\|200px]]

-	The ~~entry 3nae~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nae", 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_3nae\| PDB=3nae \| SCENE= }}

-	~~Authors: Wang, M., Beckman, J., Blaha, G., Wang, J., Konigsberg, W.H.~~	+	===RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin===

-	Description: RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 30 13~~:34:49 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20795733}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20795733 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20795733}}
		+
		+	==About this Structure==
		+	3NAE is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NAE OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20795733</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Enterobacteria phage rb69]]
		+	[[Category: Beckman, J.]]
		+	[[Category: Blaha, G.]]
		+	[[Category: Konigsberg, W H.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Wang, M.]]
		+	[[Category: Fidelity]]
		+	[[Category: Guanidinohydantoin]]
		+	[[Category: Rb69 dna polymerase]]
		+	[[Category: Transferase-dna complex]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 15 10:50:59 2010''