3bq1 - Revision history

OCA at 12:12, 30 August 2023

2023-08-30T12:12:28Z

←Older revision		Revision as of 12:12, 30 August 2023
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	<StructureSection load='3bq1' size='340' side='right'caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3bq1' size='340' side='right'caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_33909 Atcc 33909~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ1 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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3bq0\|3bq0]], [[3bq2\|3bq2]]</div>~~</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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dbh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~2285 ATCC 33909])</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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [https://pdbe.org/3bq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq1 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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [https://pdbe.org/3bq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis (By similarity).	+	[https://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 3bq1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3bq1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 33909]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pata, J D~~]]	+	[[Category: Sulfolobus acidocaldarius]]
-	[[Category: ~~Wilson, R C~~]]	+	[[Category: Pata JD]]
-	[[Category: ~~Frameshift]]~~	+	[[Category: Wilson RC]]
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Lesion bypass]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mutator protein]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Single-base deletion]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: Y-family~~]]	+

OCA at 08:21, 19 January 2022

2022-01-19T08:21:45Z

←Older revision		Revision as of 08:21, 19 January 2022
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	==Insertion ternary complex of Dbh DNA polymerase==		==Insertion ternary complex of Dbh DNA polymerase==
-	<StructureSection load='3bq1' size='340' side='right' caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3bq1' size='340' side='right'caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_33909 Atcc 33909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33909 Atcc 33909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ1 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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bq0\|3bq0]], [[3bq2\|3bq2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bq0\|3bq0]], [[3bq2\|3bq2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [~~http~~://pdbe.org/3bq1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bq1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq1 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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [https://pdbe.org/3bq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis (By similarity).	+	[[https://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 3bq1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3bq1" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 37:
	[[Category: Atcc 33909]]		[[Category: Atcc 33909]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Pata, J D]]		[[Category: Pata, J D]]
	[[Category: Wilson, R C]]		[[Category: Wilson, R C]]

OCA at 07:50, 31 October 2018

2018-10-31T07:50:25Z

←Older revision		Revision as of 07:50, 31 October 2018
Line 1:		Line 1:
		+
	==Insertion ternary complex of Dbh DNA polymerase==		==Insertion ternary complex of Dbh DNA polymerase==
	<StructureSection load='3bq1' size='340' side='right' caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3bq1' size='340' side='right' caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://pdbe.org/3bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://pdbe.org/3bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/3bq1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/3bq1_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 18:44, 9 February 2016

2016-02-09T18:44:25Z

←Older revision		Revision as of 18:44, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3bq1' size='340' side='right' caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3bq1' size='340' side='right' caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_acidocaldarius Sulfolobus acidocaldarius~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33909 Atcc 33909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ1 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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bq0\|3bq0]], [[3bq2\|3bq2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bq0\|3bq0]], [[3bq2\|3bq2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ~~Sulfolobus acidocaldarius~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://pdbe.org/3bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bq1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3bq1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33909]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Sulfolobus acidocaldarius]]
	[[Category: Pata, J D]]		[[Category: Pata, J D]]
	[[Category: Wilson, R C]]		[[Category: Wilson, R C]]

OCA at 08:46, 25 December 2014

2014-12-25T08:46:31Z

←Older revision		Revision as of 08:46, 25 December 2014
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	<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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:55, 5 November 2014

2014-11-05T10:55:50Z

←Older revision		Revision as of 10:55, 5 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ1 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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bq0\|3bq0]], [[3bq2\|3bq2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bq0\|3bq0]], [[3bq2\|3bq2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 Sulfolobus acidocaldarius])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 Sulfolobus acidocaldarius])</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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus acidocaldarius]]		[[Category: Sulfolobus acidocaldarius]]
-	[[Category: Pata, J D.]]	+	[[Category: Pata, J D]]
-	[[Category: Wilson, R C.]]	+	[[Category: Wilson, R C]]
-	[[Category: ~~-1 frameshift~~]]	+	[[Category: Frameshift]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]

OCA at 09:50, 29 September 2014

2014-09-29T09:50:26Z

←Older revision		Revision as of 09:50, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3bq1.~~png~~\|~~left~~\|200px]]	+	==Insertion ternary complex of Dbh DNA polymerase==
		+	<StructureSection load='3bq1' size='340' side='right' caption='[[3bq1]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bq1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ1 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=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bq0\|3bq0]], [[3bq2\|3bq2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 Sulfolobus acidocaldarius])</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=3bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq1 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/3bq1_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dbh is a Y family translesion DNA polymerase that accurately bypasses some damaged forms of deoxyguanosine, but also generates single-base deletion errors at frequencies of up to 50%, in specific hot spot sequences. We describe preinsertion binary, insertion ternary, and postinsertion binary crystal structures of Dbh synthesizing DNA after making a single-base deletion. The skipped template base adopts an extrahelical conformation stabilized by interactions with the C-terminal domain of the enzyme. DNA translocation and positioning of the next templating base at the active site, with space opposite to accommodate incoming nucleotide, occur independently of nucleotide binding, incorporation, and pyrophosphate release. We also show that Dbh creates single-base deletions more rapidly when the skipped base is located two or three bases upstream of the nascent base pair than when it is directly adjacent to the templating base, indicating that Dbh predominantly creates single-base deletions by template slippage rather than by dNTP-stabilized misalignment.

-	~~{{STRUCTURE_3bq1\| PDB=3bq1 \| SCENE= }}~~	+	Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.,Wilson RC, Pata JD Mol Cell. 2008 Mar 28;29(6):767-79. PMID:18374650<ref>PMID:18374650</ref>

-	~~===Insertion ternary complex~~ of ~~Dbh DNA polymerase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18374650}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3bq1]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018374650<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus acidocaldarius]]		[[Category: Sulfolobus acidocaldarius]]

OCA at 14:46, 20 October 2012

2012-10-20T14:46:46Z

←Older revision		Revision as of 14:46, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3bq1]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA].	+	[[3bq1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA].

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

OCA: Protected "3bq1" [edit=sysop:move=sysop]

2012-07-26T16:13:38Z

Protected "3bq1" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:13, 26 July 2012

OCA at 16:13, 26 July 2012

2012-07-26T16:13:37Z

←Older revision		Revision as of 16:13, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3bq1.png\|left\|200px]]		[[Image:3bq1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bq1", 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_3bq1\| PDB=3bq1 \| SCENE= }}		{{STRUCTURE_3bq1\| PDB=3bq1 \| SCENE= }}

	===Insertion ternary complex of Dbh DNA polymerase===		===Insertion ternary complex of Dbh DNA polymerase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18374650}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18374650 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18374650}}		{{ABSTRACT_PUBMED_18374650}}

	==About this Structure==		==About this Structure==
-	~~3BQ1~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA].	+	[[3bq1]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ1 OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18374650~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018374650</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus acidocaldarius]]		[[Category: Sulfolobus acidocaldarius]]
Line 42:		Line 33:
	[[Category: Single-base deletion]]		[[Category: Single-base deletion]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Transferase/dna complex]]	+	[[Category: Transferase-dna complex]]
	[[Category: Y-family]]		[[Category: Y-family]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 10:58:45 2009''