4fjj - Revision history

OCA at 11:17, 1 March 2024

OCA — Fri, 01 Mar 2024 11:17:06 GMT

←Older revision		Revision as of 11:17, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJJ FirstGlance]. <br>
-	</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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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]] 1.99Å</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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [https://pdbe.org/4fjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [https://www.ebi.ac.uk/pdbsum/4fjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjj 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=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [https://pdbe.org/4fjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [https://www.ebi.ac.uk/pdbsum/4fjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjj 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 ==
-	Current hypotheses that attempt to rationalize the high degree of base selectivity exhibited by replicative DNA polymerases (pols) concur that ternary complexes formed with incorrect dNTPs are destabilized. Knowing what accounts for this destabilization is likely to be the key to understanding base discrimination. To address this issue, we have determined crystal structures of ternary complexes with all twelve mismatches using an engineered RB69 pol quadruple mutant (qm, L415A/L561A/S565G/Y567A) that enabled us to capture nascent mispaired dNTPs. These structures show that mismatches in the Nascent base-pair Binding Pocket (NBP) of the qm pol differ markedly from mismatches embedded in binary pol-DNA complexes. Surprisingly only 3 of 12 mismatches clash with the NBP when they are modeled into the wt pol. The remaining can fit into a wt pol ternary complex but deviate from normal Watson-Crick base-pairs. Repositioning of the templating nucleotide residue and the enlarged NBP in qm ternary complex play important roles in accommodating incorrect incoming dNTPs. From these structures, we propose additional reasons as to why incorrect dNTP are incorporated so inefficiently by wild type RB69 pol: (i) steric clashes with side chains in the NBP after Fingers closing; (ii) weak interactions or large gaps between the incoming dNTP and the templating base; (iii) burying a protonated base in the hydrophobic environment of the NBP. All of these possibilities would be expected to destabilize the closed ternary complex so that incorporation of incorrect dNTP would be a rare event.

-	~~DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase.,Xia S, Wang J, Konigsberg WH J Am Chem Soc. 2012 Dec 6. PMID:23214497<ref>PMID:23214497</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 4fjj" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:52, 19 October 2022

OCA — Wed, 19 Oct 2022 19:52:29 GMT

←Older revision		Revision as of 19:52, 19 October 2022
Line 1:		Line 1:

	==RB69 DNA polymerase ternary complex with dTTP/dC==		==RB69 DNA polymerase ternary complex with dTTP/dC==
-	<StructureSection load='4fjj' size='340' side='right' caption='[[4fjj]], [[Resolution\|resolution]] 1.99Å' scene=''>	+	<StructureSection load='4fjj' size='340' side='right'caption='[[4fjj]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FJJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJJ 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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>~~	+	</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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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'>[https://proteopedia.org/fgij/fg.htm?mol=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [https://pdbe.org/4fjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [https://www.ebi.ac.uk/pdbsum/4fjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjj ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fj5\|4fj5]]~~, [[4fj7\|4fj7]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjk\|4fjk]], [[4fjl\|4fjl]], [[4fjm\|4fjm]], [[4fjn\|4fjn]], [[4fjx\|4fjx]], [[4fk0\|4fk0]], [[4fk2\|4fk2]], [[4fk4\|4fk4]]<~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">43 ([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=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [~~http~~://pdbe.org/4fjj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4fjj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjj 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 22:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4fjj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4fjj" 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: Konigsberg~~, W H~~]]	+	[[Category: Konigsberg WH]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	[[Category: Xia, S]]	+	[[Category: Xia S]]
-	~~[[Category: Dttp/dc]]~~	+
-	~~[[Category: Quadruple]]~~	+
-	~~[[Category: Rb69]]~~	+
-	~~[[Category: Rb69pol]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 07:41, 4 August 2016

OCA — Thu, 04 Aug 2016 07:41:42 GMT

←Older revision		Revision as of 07:41, 4 August 2016
Line 1:		Line 1:
		+
	==RB69 DNA polymerase ternary complex with dTTP/dC==		==RB69 DNA polymerase ternary complex with dTTP/dC==
	<StructureSection load='4fjj' size='340' side='right' caption='[[4fjj]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='4fjj' size='340' side='right' caption='[[4fjj]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJJ 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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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">[[4fj5\|4fj5]], [[4fj7\|4fj7]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjk\|4fjk]], [[4fjl\|4fjl]], [[4fjm\|4fjm]], [[4fjn\|4fjn]], [[4fjx\|4fjx]], [[4fk0\|4fk0]], [[4fk2\|4fk2]], [[4fk4\|4fk4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fj5\|4fj5]], [[4fj7\|4fj7]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjk\|4fjk]], [[4fjl\|4fjl]], [[4fjm\|4fjm]], [[4fjn\|4fjn]], [[4fjx\|4fjx]], [[4fk0\|4fk0]], [[4fk2\|4fk2]], [[4fk4\|4fk4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43 ([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 ([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=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [http://www.ebi.ac.uk/pdbsum/4fjj 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=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [http://pdbe.org/4fjj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [http://www.ebi.ac.uk/pdbsum/4fjj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 4fjj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	__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 07:00, 25 December 2014

OCA — Thu, 25 Dec 2014 07:00:36 GMT

←Older revision		Revision as of 07:00, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4fjj.~~png~~\|~~left~~\|~~200px~~]]	+	==RB69 DNA polymerase ternary complex with dTTP/dC==
		+	<StructureSection load='4fjj' size='340' side='right' caption='[[4fjj]], [[Resolution\|resolution]] 1.99Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4fjj]] 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=4FJJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJJ 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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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">[[4fj5\|4fj5]], [[4fj7\|4fj7]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjk\|4fjk]], [[4fjl\|4fjl]], [[4fjm\|4fjm]], [[4fjn\|4fjn]], [[4fjx\|4fjx]], [[4fk0\|4fk0]], [[4fk2\|4fk2]], [[4fk4\|4fk4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43 ([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=4fjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fjj RCSB], [http://www.ebi.ac.uk/pdbsum/4fjj PDBsum]</span></td></tr>
		+	</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;">
		+	== Publication Abstract from PubMed ==
		+	Current hypotheses that attempt to rationalize the high degree of base selectivity exhibited by replicative DNA polymerases (pols) concur that ternary complexes formed with incorrect dNTPs are destabilized. Knowing what accounts for this destabilization is likely to be the key to understanding base discrimination. To address this issue, we have determined crystal structures of ternary complexes with all twelve mismatches using an engineered RB69 pol quadruple mutant (qm, L415A/L561A/S565G/Y567A) that enabled us to capture nascent mispaired dNTPs. These structures show that mismatches in the Nascent base-pair Binding Pocket (NBP) of the qm pol differ markedly from mismatches embedded in binary pol-DNA complexes. Surprisingly only 3 of 12 mismatches clash with the NBP when they are modeled into the wt pol. The remaining can fit into a wt pol ternary complex but deviate from normal Watson-Crick base-pairs. Repositioning of the templating nucleotide residue and the enlarged NBP in qm ternary complex play important roles in accommodating incorrect incoming dNTPs. From these structures, we propose additional reasons as to why incorrect dNTP are incorporated so inefficiently by wild type RB69 pol: (i) steric clashes with side chains in the NBP after Fingers closing; (ii) weak interactions or large gaps between the incoming dNTP and the templating base; (iii) burying a protonated base in the hydrophobic environment of the NBP. All of these possibilities would be expected to destabilize the closed ternary complex so that incorporation of incorrect dNTP would be a rare event.

-	~~{{STRUCTURE_4fjj\| PDB=4fjj \| SCENE= }}~~	+	DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase.,Xia S, Wang J, Konigsberg WH J Am Chem Soc. 2012 Dec 6. PMID:23214497<ref>PMID:23214497</ref>

-	~~===RB69 DNA polymerase ternary complex with dTTP~~/~~dC===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23214497}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[4fjj]] 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=4FJJ OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[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: Dttp/dc]]		[[Category: Dttp/dc]]
	[[Category: Quadruple]]		[[Category: Quadruple]]

OCA at 12:04, 6 February 2013

OCA — Wed, 06 Feb 2013 12:04:17 GMT

←Older revision		Revision as of 12:04, 6 February 2013
Line 9:		Line 9:
	==About this Structure==		==About this Structure==
	[[4fjj]] 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=4FJJ OCA].		[[4fjj]] 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=4FJJ OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]

OCA at 12:50, 30 January 2013

OCA — Wed, 30 Jan 2013 12:50:10 GMT

←Older revision		Revision as of 12:50, 30 January 2013
Line 1:		Line 1:
-	[[Image:4fjj.~~jpg~~\|left\|200px]]	+	[[Image:4fjj.png\|left\|200px]]

	{{STRUCTURE_4fjj\| PDB=4fjj \| SCENE= }}		{{STRUCTURE_4fjj\| PDB=4fjj \| SCENE= }}

OCA at 11:26, 19 December 2012

OCA — Wed, 19 Dec 2012 11:26:31 GMT

←Older revision		Revision as of 11:26, 19 December 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4fjj.jpg\|left\|200px]]

-	~~The entry~~ 4fjj ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4fjj\| PDB=4fjj \| SCENE= }}

-	~~Authors: Xia, S., Wang, J., Konigsberg, W.H.~~	+	===RB69 DNA polymerase ternary complex with dTTP/dC===

-	~~Description~~: ~~RB69~~ DNA polymerase ~~ternary complex with dTTP~~/dC	+	{{ABSTRACT_PUBMED_23214497}}
		+
		+	==About this Structure==
		+	[[4fjj]] 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=4FJJ OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Enterobacteria phage rb69]]
		+	[[Category: Konigsberg, W H.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Xia, S.]]
		+	[[Category: Dttp/dc]]
		+	[[Category: Quadruple]]
		+	[[Category: Rb69]]
		+	[[Category: Rb69pol]]
		+	[[Category: Transferase-dna complex]]

OCA at 04:53, 8 August 2012

OCA — Wed, 08 Aug 2012 04:53:23 GMT

←Older revision		Revision as of 04:53, 8 August 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4fjj is ON HOLD	+	The entry 4fjj 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 dTTP/dC		Description: RB69 DNA polymerase ternary complex with dTTP/dC

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

OCA — Wed, 20 Jun 2012 07:27:22 GMT

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

←Older revision

Revision as of 07:27, 20 June 2012

OCA: New page: '''Unreleased structure''' The entry 4fjj is ON HOLD Authors: Xia, S., Wang, J., Konigsberg, W.H. Description: RB69 DNA polymerase ternary complex with dTTP/dC

OCA — Wed, 20 Jun 2012 07:27:21 GMT

New page: '''Unreleased structure''' The entry 4fjj is ON HOLD Authors: Xia, S., Wang, J., Konigsberg, W.H. Description: RB69 DNA polymerase ternary complex with dTTP/dC

New page

'''Unreleased structure'''

The entry 4fjj is ON HOLD

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

Description: RB69 DNA polymerase ternary complex with dTTP/dC