4dtn - Revision history

OCA at 10:56, 1 March 2024

OCA — Fri, 01 Mar 2024 10:56:50 GMT

←Older revision		Revision as of 10:56, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DTN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DTN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <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]] 1.96Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [https://pdbe.org/4dtn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [https://www.ebi.ac.uk/pdbsum/4dtn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dtn 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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [https://pdbe.org/4dtn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [https://www.ebi.ac.uk/pdbsum/4dtn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dtn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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.	+	[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.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	During DNA synthesis base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base-pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the Penultimate Base-pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The incorporation efficiency for incoming dNTPs opposite an abasic site varied between 2 and 210 fold depending on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporations were consistent with specific features of base-stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex and the incorporation efficiency of incoming dNTPs is reduced.	+

-	Contribution of Partial Charge Interactions and Base-Stacking to the Efficiency of Primer-Extension at and beyond Abasic Sites in DNA.,Xia S, Vashishtha AK, Bulkley D, Eom SH, Wang J, Konigsberg WH Biochemistry. 2012 May 25. PMID:22630605<ref>PMID:22630605</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 4dtn" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:38, 21 September 2022

OCA — Wed, 21 Sep 2022 08:38:12 GMT

←Older revision		Revision as of 08:38, 21 September 2022
Line 3:		Line 3:
	<StructureSection load='4dtn' size='340' side='right'caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='4dtn' size='340' side='right'caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DTN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DTN 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" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene><~~/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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [https://pdbe.org/4dtn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [https://www.ebi.ac.uk/pdbsum/4dtn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dtn ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4dtj\|4dtj]]~~, ~~[[4dtm\|4dtm]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4du3\|4du3]], [[4du4\|4du4]]~~<~~/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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [~~http~~://pdbe.org/4dtn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dtn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dtn 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4dtn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4dtn" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpr69]]~~	+	[[Category: Escherichia phage RB69]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Konigsberg~~, W H~~]]	+	[[Category: Konigsberg WH]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	[[Category: Xia, S]]	+	[[Category: Xia S]]
-	~~[[Category: Abasic site]]~~	+
-	~~[[Category: Datp]]~~	+
-	~~[[Category: Rb69pol]]~~	+
-	~~[[Category: Thf]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 07:48, 27 March 2019

OCA — Wed, 27 Mar 2019 07:48:11 GMT

←Older revision		Revision as of 07:48, 27 March 2019
Line 1:		Line 1:

	==RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==		==RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==
-	<StructureSection load='4dtn' size='340' side='right' caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>	+	<StructureSection load='4dtn' size='340' side='right'caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN FirstGlance]. <br>
Line 30:		Line 30:
	[[Category: Bpr69]]		[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Konigsberg, W H]]		[[Category: Konigsberg, W H]]
	[[Category: Wang, J]]		[[Category: Wang, J]]

OCA at 21:31, 5 August 2016

OCA — Fri, 05 Aug 2016 21:31:22 GMT

←Older revision		Revision as of 21:31, 5 August 2016
Line 1:		Line 1:
		+
	==RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==		==RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==
	<StructureSection load='4dtn' size='340' side='right' caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='4dtn' size='340' side='right' caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN 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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4du3\|4du3]], [[4du4\|4du4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4du3\|4du3]], [[4du4\|4du4]]</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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [http://www.ebi.ac.uk/pdbsum/4dtn 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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [http://pdbe.org/4dtn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [http://www.ebi.ac.uk/pdbsum/4dtn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dtn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4dtn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpr69]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Enterobacteria phage rb69]]
	[[Category: Konigsberg, W H]]		[[Category: Konigsberg, W H]]
	[[Category: Wang, J]]		[[Category: Wang, J]]

OCA at 22:04, 25 December 2014

OCA — Thu, 25 Dec 2014 22:04:30 GMT

←Older revision		Revision as of 22:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN FirstGlance]. <br>
-	</td></tr><tr><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><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><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4du3\|4du3]], [[4du4\|4du4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4du3\|4du3]], [[4du4\|4du4]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [http://www.ebi.ac.uk/pdbsum/4dtn 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=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [http://www.ebi.ac.uk/pdbsum/4dtn 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]
-	[[Category: Konigsberg, W H.]]	+	[[Category: Konigsberg, W H]]
-	[[Category: Wang, J.]]	+	[[Category: Wang, J]]
-	[[Category: Xia, S.]]	+	[[Category: Xia, S]]
	[[Category: Abasic site]]		[[Category: Abasic site]]
	[[Category: Datp]]		[[Category: Datp]]

OCA at 06:54, 25 June 2014

OCA — Wed, 25 Jun 2014 06:54:58 GMT

←Older revision		Revision as of 06:54, 25 June 2014
Line 1:		Line 1:
-	[[~~Image:~~4dtn.~~png~~\|~~left~~\|~~200px~~]]	+	==RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==
		+	<StructureSection load='4dtn' size='340' side='right' caption='[[4dtn]], [[Resolution\|resolution]] 1.96Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dtn]] 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=4DTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTN FirstGlance]. <br>
		+	</td></tr><tr><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><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4du3\|4du3]], [[4du4\|4du4]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dtn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dtn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dtn RCSB], [http://www.ebi.ac.uk/pdbsum/4dtn PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During DNA synthesis base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base-pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the Penultimate Base-pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The incorporation efficiency for incoming dNTPs opposite an abasic site varied between 2 and 210 fold depending on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporations were consistent with specific features of base-stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex and the incorporation efficiency of incoming dNTPs is reduced.

-	~~{{STRUCTURE_4dtn\| PDB=4dtn \| SCENE= }}~~	+	Contribution of Partial Charge Interactions and Base-Stacking to the Efficiency of Primer-Extension at and beyond Abasic Sites in DNA.,Xia S, Vashishtha AK, Bulkley D, Eom SH, Wang J, Konigsberg WH Biochemistry. 2012 May 25. PMID:22630605<ref>PMID:22630605</ref>

-	~~===RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA~~/~~dT as~~ the ~~Penultimate Base-pair===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22630605}}~~	+	==See Also==
-		+	*[[DNA polymerase\|DNA polymerase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4dtn~~]] 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=4DTN OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022630605<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]

OCA at 05:49, 5 September 2012

OCA — Wed, 05 Sep 2012 05:49:53 GMT

←Older revision		Revision as of 05:49, 5 September 2012
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-	[[Image:4dtn.~~jpg~~\|left\|200px]]	+	[[Image:4dtn.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_4dtn", 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_4dtn\| PDB=4dtn \| SCENE= }}		{{STRUCTURE_4dtn\| PDB=4dtn \| SCENE= }}

	===RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair===		===RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22630605}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22630605 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22630605}}		{{ABSTRACT_PUBMED_22630605}}

OCA at 07:45, 6 June 2012

OCA — Wed, 06 Jun 2012 07:45:33 GMT

←Older revision		Revision as of 07:45, 6 June 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4dtn.jpg\|left\|200px]]

-	The ~~entry 4dtn~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4dtn", 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_4dtn\| PDB=4dtn \| SCENE= }}

-	~~Authors: Xia, S., Wang, J., Konigsberg, W.H.~~	+	===RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair===

-	~~Description~~: ~~RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA~~/~~dT as~~ the ~~Penultimate Base~~-~~pair~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22630605}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22630605 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22630605}}
		+
		+	==About this Structure==
		+	[[4dtn]] 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=4DTN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022630605</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Enterobacteria phage rb69]]
		+	[[Category: Konigsberg, W H.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Xia, S.]]
		+	[[Category: Abasic site]]
		+	[[Category: Datp]]
		+	[[Category: Rb69pol]]
		+	[[Category: Thf]]
		+	[[Category: Transferase-dna complex]]

OCA at 07:12, 21 March 2012

OCA — Wed, 21 Mar 2012 07:12:45 GMT

←Older revision		Revision as of 07:12, 21 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dtn is ON HOLD	+	The entry 4dtn is ON HOLD until Paper Publication

	Authors: Xia, S., Wang, J., Konigsberg, W.H.		Authors: Xia, S., Wang, J., Konigsberg, W.H.

	Description: RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair		Description: RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair

OCA: Protected "4dtn" [edit=sysop:move=sysop]

OCA — Wed, 29 Feb 2012 08:27:25 GMT

Protected "4dtn" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:27, 29 February 2012