4e3s - Revision history

OCA at 11:01, 1 March 2024

2024-03-01T11:01:36Z

←Older revision		Revision as of 11:01, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E3S FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E3S 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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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]] 2.04Å</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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [https://pdbe.org/4e3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [https://www.ebi.ac.uk/pdbsum/4e3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e3s 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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [https://pdbe.org/4e3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [https://www.ebi.ac.uk/pdbsum/4e3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e3s 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 ==~~	+
-	Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10(2)-10(3)-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n - 2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.	+

-	~~Probing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA.,Xia S, Christian TD, Wang J, Konigsberg WH Biochemistry. 2012 May 17. PMID:22571765<ref>PMID:22571765</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 4e3s" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:47, 28 September 2022

2022-09-28T06:47:55Z

←Older revision		Revision as of 06:47, 28 September 2022
Line 1:		Line 1:

	==RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT==		==RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT==
-	<StructureSection load='4e3s' size='340' side='right' caption='[[4e3s]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='4e3s' size='340' side='right'caption='[[4e3s]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E3S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E3S 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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [https://pdbe.org/4e3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [https://www.ebi.ac.uk/pdbsum/4e3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e3s ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dtn\|4dtn]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4du3\|4du3]], [[4du4\|4du4]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4eav\|4eav]]</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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [~~http~~://pdbe.org/4e3s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e3s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e3s 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 4e3s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4e3s" 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: Dqtp]]~~	+
-	~~[[Category: Rb69pol]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 09:50, 5 August 2016

2016-08-05T09:50:25Z

←Older revision		Revision as of 09:50, 5 August 2016
Line 1:		Line 1:
		+
	==RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT==		==RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT==
	<StructureSection load='4e3s' size='340' side='right' caption='[[4e3s]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='4e3s' size='340' side='right' caption='[[4e3s]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E3S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E3S 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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dtn\|4dtn]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4du3\|4du3]], [[4du4\|4du4]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4eav\|4eav]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dtn\|4dtn]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4du3\|4du3]], [[4du4\|4du4]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4eav\|4eav]]</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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [http://www.ebi.ac.uk/pdbsum/4e3s 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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [http://pdbe.org/4e3s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [http://www.ebi.ac.uk/pdbsum/4e3s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e3s 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 4e3s" 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 17:49, 25 December 2014

2014-12-25T17:49:38Z

←Older revision		Revision as of 17:49, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E3S FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E3S 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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</scene></td></tr>
-	<tr><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dtn\|4dtn]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4du3\|4du3]], [[4du4\|4du4]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4eav\|4eav]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dtn\|4dtn]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4du3\|4du3]], [[4du4\|4du4]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4eav\|4eav]]</td></tr>
-	<tr><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 Enterobacteria phage RB69])</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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [http://www.ebi.ac.uk/pdbsum/4e3s 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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [http://www.ebi.ac.uk/pdbsum/4e3s 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 27:		Line 29:
	[[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: Dqtp]]		[[Category: Dqtp]]
	[[Category: Rb69pol]]		[[Category: Rb69pol]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 09:28, 11 June 2014

2014-06-11T09:28:23Z

←Older revision		Revision as of 09:28, 11 June 2014
Line 1:		Line 1:
-	[[~~Image:~~4e3s.~~png~~\|~~left~~\|~~200px~~]]	+	==RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT==
		+	<StructureSection load='4e3s' size='340' side='right' caption='[[4e3s]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4e3s]] 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=4E3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E3S 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=QTP:3-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-7-METHYL-3H-IMIDAZO[4,5-B]PYRIDINE'>QTP</scene><br>
		+	<tr><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dtj\|4dtj]], [[4dtm\|4dtm]], [[4dtn\|4dtn]], [[4dto\|4dto]], [[4dtp\|4dtp]], [[4dtr\|4dtr]], [[4dts\|4dts]], [[4dtu\|4dtu]], [[4du3\|4du3]], [[4du4\|4du4]], [[4dtx\|4dtx]], [[4du1\|4du1]], [[4eav\|4eav]]</td></tr>
		+	<tr><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><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=4e3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e3s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e3s RCSB], [http://www.ebi.ac.uk/pdbsum/4e3s PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10(2)-10(3)-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n - 2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.

-	~~{{STRUCTURE_4e3s\| PDB=4e3s \| SCENE= }}~~	+	Probing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA.,Xia S, Christian TD, Wang J, Konigsberg WH Biochemistry. 2012 May 17. PMID:22571765<ref>PMID:22571765</ref>

-	~~===RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22571765}}~~	+	==See Also==
-		+	*[[DNA polymerase\|DNA polymerase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4e3s~~]] 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=4E3S OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022571765<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]

OCA at 05:04, 15 August 2012

2012-08-15T05:04:04Z

←Older revision		Revision as of 05:04, 15 August 2012
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-	[[Image:4e3s.~~jpg~~\|left\|200px]]	+	[[Image:4e3s.png\|left\|200px]]

-	<!--
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-	-->
	{{STRUCTURE_4e3s\| PDB=4e3s \| SCENE= }}		{{STRUCTURE_4e3s\| PDB=4e3s \| SCENE= }}

	===RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT===		===RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT===

-
-	<!--
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-	(as it appears on PubMed at http://www.pubmed.gov), where 22571765 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_22571765}}		{{ABSTRACT_PUBMED_22571765}}

OCA at 06:07, 23 May 2012

2012-05-23T06:07:52Z

←Older revision		Revision as of 06:07, 23 May 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4e3s.jpg\|left\|200px]]

-	The ~~entry 4e3s~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4e3s", 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_4e3s\| PDB=4e3s \| SCENE= }}

-	~~Authors: Xia, S., Wang, J., Konigsberg, W.H.~~	+	===RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT===

-	~~Description~~: ~~RB69 DNA Polymerase Ternary Complex~~ with ~~dQTP Opposite dT~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22571765}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22571765 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22571765}}
		+
		+	==About this Structure==
		+	[[4e3s]] 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=4E3S OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022571765</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Enterobacteria phage rb69]]
		+	[[Category: Konigsberg, W H.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Xia, S.]]
		+	[[Category: Dqtp]]
		+	[[Category: Rb69pol]]
		+	[[Category: Transferase-dna complex]]

OCA at 06:38, 11 April 2012

2012-04-11T06:38:38Z

←Older revision		Revision as of 06:38, 11 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4e3s is ON HOLD	+	The entry 4e3s 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 dQTP Opposite dT		Description: RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT

OCA at 05:44, 4 April 2012

2012-04-04T05:44:54Z

←Older revision		Revision as of 05:44, 4 April 2012
Line 3:		Line 3:
	The entry 4e3s is ON HOLD		The entry 4e3s is ON HOLD

-	Authors: Xia, S., Wang, J., ~~Kongisberg~~, W.	+	Authors: Xia, S., Wang, J., Konigsberg, W.H.

	Description: RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT		Description: RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT

OCA: Protected "4e3s" [edit=sysop:move=sysop]

2012-03-21T07:16:08Z

Protected "4e3s" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:16, 21 March 2012