4fj7 - Revision history

OCA at 11:16, 1 March 2024

OCA — Fri, 01 Mar 2024 11:16:57 GMT

←Older revision		Revision as of 11:16, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJ7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJ7 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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='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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [https://pdbe.org/4fj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [https://www.ebi.ac.uk/pdbsum/4fj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fj7 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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [https://pdbe.org/4fj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [https://www.ebi.ac.uk/pdbsum/4fj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fj7 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 4fj7" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:52, 19 October 2022

OCA — Wed, 19 Oct 2022 19:52:04 GMT

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

	==RB69 DNA polymerase ternary complex with dGTP/dT==		==RB69 DNA polymerase ternary complex with dGTP/dT==
-	<StructureSection load='4fj7' size='340' side='right' caption='[[4fj7]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4fj7' size='340' side='right'caption='[[4fj7]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FJ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJ7 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fj5\|4fj5]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjj\|4fjj]], [[4fjk\|4fjk]], [[4fjl\|4fjl]], [[4fjm\|4fjm]], [[4fjn\|4fjn]], [[4fjx\|4fjx]], [[4fk0\|4fk0]], [[4fk2\|4fk2]], [[4fk4\|4fk4]]</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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [https://pdbe.org/4fj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [https://www.ebi.ac.uk/pdbsum/4fj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fj7 ProSAT]</span></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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [~~http~~://pdbe.org/4fj7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4fj7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4fj7 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 4fj7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4fj7" 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: Dgtp/dt]]~~	+
-	~~[[Category: Quadruple]]~~	+
-	~~[[Category: Rb69]]~~	+
-	~~[[Category: Rb69pol]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 14:03, 4 August 2016

OCA — Thu, 04 Aug 2016 14:03:37 GMT

←Older revision		Revision as of 14:03, 4 August 2016
Line 1:		Line 1:
		+
	==RB69 DNA polymerase ternary complex with dGTP/dT==		==RB69 DNA polymerase ternary complex with dGTP/dT==
	<StructureSection load='4fj7' size='340' side='right' caption='[[4fj7]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4fj7' size='340' side='right' caption='[[4fj7]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJ7 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fj5\|4fj5]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjj\|4fjj]], [[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]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjj\|4fjj]], [[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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [http://www.ebi.ac.uk/pdbsum/4fj7 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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [http://pdbe.org/4fj7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [http://www.ebi.ac.uk/pdbsum/4fj7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fj7 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 4fj7" 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 09:58, 25 December 2014

OCA — Thu, 25 Dec 2014 09:58:46 GMT

←Older revision		Revision as of 09:58, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4fj7.~~png~~\|~~left~~\|~~200px~~]]	+	==RB69 DNA polymerase ternary complex with dGTP/dT==
		+	<StructureSection load='4fj7' size='340' side='right' caption='[[4fj7]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4fj7]] 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=4FJ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJ7 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fj5\|4fj5]], [[4fj8\|4fj8]], [[4fj9\|4fj9]], [[4fjg\|4fjg]], [[4fjh\|4fjh]], [[4fji\|4fji]], [[4fjj\|4fjj]], [[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=4fj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fj7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fj7 RCSB], [http://www.ebi.ac.uk/pdbsum/4fj7 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_4fj7\| PDB=4fj7 \| 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 dGTP~~/~~dT===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23214497}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[4fj7]] 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=4FJ7 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: Dgtp/dt]]		[[Category: Dgtp/dt]]
	[[Category: Quadruple]]		[[Category: Quadruple]]

OCA at 11:53, 6 February 2013

OCA — Wed, 06 Feb 2013 11:53:03 GMT

←Older revision		Revision as of 11:53, 6 February 2013
Line 9:		Line 9:
	==About this Structure==		==About this Structure==
	[[4fj7]] 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=4FJ7 OCA].		[[4fj7]] 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=4FJ7 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 12:49, 30 January 2013

OCA — Wed, 30 Jan 2013 12:49:54 GMT

←Older revision		Revision as of 12:49, 30 January 2013
Line 1:		Line 1:
-	[[Image:4fj7.~~jpg~~\|left\|200px]]	+	[[Image:4fj7.png\|left\|200px]]

	{{STRUCTURE_4fj7\| PDB=4fj7 \| SCENE= }}		{{STRUCTURE_4fj7\| PDB=4fj7 \| SCENE= }}

OCA at 11:26, 19 December 2012

OCA — Wed, 19 Dec 2012 11:26:27 GMT

←Older revision		Revision as of 11:26, 19 December 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4fj7.jpg\|left\|200px]]

-	~~The entry~~ 4fj7 ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4fj7\| PDB=4fj7 \| SCENE= }}

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

-	~~Description~~: ~~RB69~~ DNA polymerase ~~ternary complex with dGTP~~/dT	+	{{ABSTRACT_PUBMED_23214497}}
		+
		+	==About this Structure==
		+	[[4fj7]] 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=4FJ7 OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Enterobacteria phage rb69]]
		+	[[Category: Konigsberg, W H.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Xia, S.]]
		+	[[Category: Dgtp/dt]]
		+	[[Category: Quadruple]]
		+	[[Category: Rb69]]
		+	[[Category: Rb69pol]]
		+	[[Category: Transferase-dna complex]]

OCA at 05:24, 1 August 2012

OCA — Wed, 01 Aug 2012 05:24:18 GMT

←Older revision		Revision as of 05:24, 1 August 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4fj7 is ON HOLD	+	The entry 4fj7 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 dGTP/dT		Description: RB69 DNA polymerase ternary complex with dGTP/dT

OCA: Protected "4fj7" [edit=sysop:move=sysop]

OCA — Wed, 20 Jun 2012 07:27:01 GMT

Protected "4fj7" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:27, 20 June 2012

OCA: New page: '''Unreleased structure''' The entry 4fj7 is ON HOLD Authors: Xia, S., Wang, J., Konigsberg, W.H. Description: RB69 DNA polymerase ternary complex with dGTP/dT

OCA — Wed, 20 Jun 2012 07:27:00 GMT

New page: '''Unreleased structure''' The entry 4fj7 is ON HOLD Authors: Xia, S., Wang, J., Konigsberg, W.H. Description: RB69 DNA polymerase ternary complex with dGTP/dT

New page

'''Unreleased structure'''

The entry 4fj7 is ON HOLD

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

Description: RB69 DNA polymerase ternary complex with dGTP/dT