3sq2 - Revision history

OCA at 09:54, 1 March 2024

2024-03-01T09:54:28Z

←Older revision		Revision as of 09:54, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3sq2' size='340' side='right'caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3sq2' size='340' side='right'caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sq2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpr69 Bpr69~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sq2]] 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=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SQ2 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=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]] 2.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sq4\|3sq4]]~~, ~~[[3sun\|3sun]], [[3suo\|3suo]], [[3sup\|3sup]], [[3suq\|3suq]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">43 ([https://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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [https://pdbe.org/3sq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [https://www.ebi.ac.uk/pdbsum/3sq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sq2 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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [https://pdbe.org/3sq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [https://www.ebi.ac.uk/pdbsum/3sq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sq2 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 ==~~	+
-	The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased "breathing" at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.	+

-	Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase.,Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W Biochemistry. 2011 Nov 22;50(46):10136-49. Epub 2011 Oct 28. PMID:22023103<ref>PMID:22023103</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 3sq2" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== 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: 2-aminopurine]]~~	+
-	~~[[Category: At rich]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:05, 29 June 2022

2022-06-29T08:05:46Z

←Older revision		Revision as of 08:05, 29 June 2022
Line 1:		Line 1:

	==RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)==		==RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)==
-	<StructureSection load='3sq2' size='340' side='right' caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3sq2' size='340' side='right'caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sq2]] 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=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sq2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SQ2 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=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=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sq4\|3sq4]], [[3sun\|3sun]], [[3suo\|3suo]], [[3sup\|3sup]], [[3suq\|3suq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sq4\|3sq4]], [[3sun\|3sun]], [[3suo\|3suo]], [[3sup\|3sup]], [[3suq\|3suq]]</div></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">43 ([https://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'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [~~http~~://pdbe.org/3sq2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3sq2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3sq2 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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [https://pdbe.org/3sq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [https://www.ebi.ac.uk/pdbsum/3sq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sq2 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 22:
	</div>		</div>
	<div class="pdbe-citations 3sq2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3sq2" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 28:
	[[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 11:31, 5 August 2016

2016-08-05T11:31:59Z

←Older revision		Revision as of 11:31, 5 August 2016
Line 1:		Line 1:
		+
	==RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)==		==RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)==
	<StructureSection load='3sq2' size='340' side='right' caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3sq2' size='340' side='right' caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sq2]] 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=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sq2]] 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=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SQ2 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=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sq4\|3sq4]], [[3sun\|3sun]], [[3suo\|3suo]], [[3sup\|3sup]], [[3suq\|3suq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sq4\|3sq4]], [[3sun\|3sun]], [[3suo\|3suo]], [[3sup\|3sup]], [[3suq\|3suq]]</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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [http://www.ebi.ac.uk/pdbsum/3sq2 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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [http://pdbe.org/3sq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [http://www.ebi.ac.uk/pdbsum/3sq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sq2 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 3sq2" 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 02:03, 25 December 2014

2014-12-25T02:03:21Z

←Older revision		Revision as of 02:03, 25 December 2014
Line 10:		Line 10:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [http://www.ebi.ac.uk/pdbsum/3sq2 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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [http://www.ebi.ac.uk/pdbsum/3sq2 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 ==

OCA at 12:03, 9 December 2014

2014-12-09T12:03:56Z

←Older revision		Revision as of 12:03, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3sq2.~~png~~\|~~left~~\|~~200px~~]]	+	==RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)==
		+	<StructureSection load='3sq2' size='340' side='right' caption='[[3sq2]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3sq2]] 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=3SQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SQ2 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=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sq4\|3sq4]], [[3sun\|3sun]], [[3suo\|3suo]], [[3sup\|3sup]], [[3suq\|3suq]]</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=3sq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sq2 RCSB], [http://www.ebi.ac.uk/pdbsum/3sq2 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased "breathing" at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.

-	~~{{STRUCTURE_3sq2\| PDB=3sq2 \| SCENE= }}~~	+	Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase.,Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W Biochemistry. 2011 Nov 22;50(46):10136-49. Epub 2011 Oct 28. PMID:22023103<ref>PMID:22023103</ref>

-	~~===RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22023103}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3sq2]] 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=3SQ2 OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:022023103<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]
-	[[Category: Konigsberg, W H.]]	+	[[Category: Konigsberg, W H]]
-	[[Category: Wang, J.]]	+	[[Category: Wang, J]]
-	[[Category: Xia, S.]]	+	[[Category: Xia, S]]
	[[Category: 2-aminopurine]]		[[Category: 2-aminopurine]]
	[[Category: At rich]]		[[Category: At rich]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 11:25, 20 October 2012

2012-10-20T11:25:49Z

←Older revision		Revision as of 11:25, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3sq2]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SQ2 OCA].	+	[[3sq2]] 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=3SQ2 OCA].

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

OCA at 05:20, 26 July 2012

2012-07-26T05:20:18Z

←Older revision		Revision as of 05:20, 26 July 2012
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	[[Image:3sq2.png\|left\|200px]]		[[Image:3sq2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3sq2", 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_3sq2\| PDB=3sq2 \| SCENE= }}		{{STRUCTURE_3sq2\| PDB=3sq2 \| SCENE= }}

	===RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)===		===RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22023103}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22023103 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_22023103}}		{{ABSTRACT_PUBMED_22023103}}

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	==See Also==		==See Also==
-	*[[DNA polymerase]]	+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==

OCA at 05:27, 30 November 2011

2011-11-30T05:27:48Z

←Older revision		Revision as of 05:27, 30 November 2011
Line 19:		Line 19:

	==About this Structure==		==About this Structure==
-	[[3sq2]] 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=3SQ2 OCA].	+	[[3sq2]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SQ2 OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase]]

	==Reference==		==Reference==

OCA at 11:14, 16 November 2011

2011-11-16T11:14:51Z

←Older revision		Revision as of 11:14, 16 November 2011
Line 1:		Line 1:
-	[[Image:3sq2.~~jpg~~\|left\|200px]]	+	[[Image:3sq2.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)===		===RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22023103}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22023103 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22023103}}

	==About this Structure==		==About this Structure==
	[[3sq2]] 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=3SQ2 OCA].		[[3sq2]] 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=3SQ2 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022023103</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Enterobacteria phage rb69]]		[[Category: Enterobacteria phage rb69]]

OCA at 11:49, 9 November 2011

2011-11-09T11:49:10Z

←Older revision		Revision as of 11:49, 9 November 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3sq2.jpg\|left\|200px]]

-	The ~~entry 3sq2~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3sq2", 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_3sq2\| PDB=3sq2 \| SCENE= }}

-	~~Authors: Xia, S., Konigsberg, W.H., Wang, J.~~	+	===RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)===

-	~~Description~~: ~~RB69~~ DNA ~~Polymerase Ternary Complex with dTTP Opposite 2AP (AT~~ rich ~~sequence)~~	+
		+	==About this Structure==
		+	[[3sq2]] 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=3SQ2 OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Enterobacteria phage rb69]]
		+	[[Category: Konigsberg, W H.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Xia, S.]]
		+	[[Category: 2-aminopurine]]
		+	[[Category: At rich]]
		+	[[Category: Transferase-dna complex]]