2c2d - Revision history

OCA at 14:03, 13 December 2023

2023-12-13T14:03:09Z

← Older revision		Revision as of 14:03, 13 December 2023
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	<StructureSection load='2c2d' size='340' side='right'caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='2c2d' size='340' side='right'caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Sulso Sulso~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2D 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=DTP:~~2~~-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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]] 2.57Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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;'>[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]]~~, [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]<~~/div></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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [https://pdbe.org/2c2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [https://www.ebi.ac.uk/pdbsum/2c2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2d 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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [https://pdbe.org/2c2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [https://www.ebi.ac.uk/pdbsum/2c2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2d ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] 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. It is involved in translesional synthesis.
	== 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 2c2d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: DNA-directed DNA polymerase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Sulso~~]]		[[Category: Saccharolobus solfataricus P2]]
	[[Category: ~~Egli, M~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Irimia, A~~]]		[[Category: Egli M]]
	[[Category: ~~Loukachevitch, L V~~]]		[[Category: Irimia A]]
	[[Category: ~~8-oxo-2p-deoxy-guanosine-5p- monophosphate]]~~		[[Category: Loukachevitch LV]]
	~~[[Category: Datp]]~~
	~~[[Category: Dna damage]]~~
	~~[[Category: Dna repair]]~~
	~~[[Category: Dna replication]]~~
	~~[[Category: Dna-binding]]~~
	~~[[Category: Dna-directed dna polymerase]]~~
	~~[[Category: Magnesium]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Mutator protein]]~~
	~~[[Category: Nucleotidyltransferase]]~~
	~~[[Category: P2 dna polymerase iv]]~~
	~~[[Category: Polymerase]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Translesion dna polymerase~~]]

OCA at 09:59, 26 May 2021

2021-05-26T09:59:40Z

← Older revision		Revision as of 09:59, 26 May 2021
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	<StructureSection load='2c2d' size='340' side='right'caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='2c2d' size='340' side='right'caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2C2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2D 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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</div></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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [~~http~~://pdbe.org/2c2d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2c2d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2d 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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [https://pdbe.org/2c2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [https://www.ebi.ac.uk/pdbsum/2c2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:44, 21 August 2019

2019-08-21T07:44:35Z

← Older revision		Revision as of 07:44, 21 August 2019
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	==Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==		==Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
	<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='2c2d' size='340' side='right'caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D FirstGlance]. <br>
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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/c2/2c2d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/2c2d_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>
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	</div>		</div>
	<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
			[[Category: Large Structures]]
	[[Category: Sulso]]		[[Category: Sulso]]
	[[Category: Egli, M]]		[[Category: Egli, M]]

OCA at 14:16, 16 November 2017

2017-11-16T14:16:56Z

← Older revision		Revision as of 14:16, 16 November 2017
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	==Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==		==Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
	<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://pdbe.org/2c2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d 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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://pdbe.org/2c2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2c2d" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:08, 10 February 2016

2016-02-10T02:08:10Z

← Older revision		Revision as of 02:08, 10 February 2016
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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=2c2d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:26, 30 November 2015

2015-11-30T21:26:20Z

← Older revision		Revision as of 21:26, 30 November 2015
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	==~~EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE~~ 7,8-~~DIHYDRO~~-8-~~OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS~~ DNA ~~POLYMERASE DPO4~~==		==Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4==
	<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 04:19, 11 September 2015

2015-09-11T04:19:12Z

← Older revision		Revision as of 04:19, 11 September 2015
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	<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus Sulfolobus solfataricus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D 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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d 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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://pdbe.org/2c2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2c2d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: ~~Sulfolobus solfataricus~~]]		[[Category: Sulso]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Irimia, A]]		[[Category: Irimia, A]]

OCA at 18:29, 15 January 2015

2015-01-15T18:29:31Z

← Older revision		Revision as of 18:29, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D 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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d 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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d 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 solfataricus]]		[[Category: Sulfolobus solfataricus]]
	[[Category: Egli, M.]]		[[Category: Egli, M]]
	[[Category: Irimia, A.]]		[[Category: Irimia, A]]
	[[Category: Loukachevitch, L V.]]		[[Category: Loukachevitch, L V]]
	[[Category: 8-oxo-2p-deoxy-guanosine-5p- monophosphate]]		[[Category: 8-oxo-2p-deoxy-guanosine-5p- monophosphate]]
	[[Category: Datp]]		[[Category: Datp]]

OCA at 10:23, 29 September 2014

2014-09-29T10:23:09Z

← Older revision		Revision as of 10:23, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2c2d~~.~~png~~\|~~left~~\|~~200px~~]]		==EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8-OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4==
			<StructureSection load='2c2d' size='340' side='right' caption='[[2c2d]], [[Resolution\|resolution]] 2.57Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2D 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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1jxl\|1jxl]], [[1n48\|1n48]], [[1n56\|1n56]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[1s10\|1s10]], [[1s97\|1s97]], [[1s9f\|1s9f]], [[2ago\|2ago]], [[2agp\|2agp]], [[2agq\|2agq]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]], [[2br0\|2br0]], [[2c22\|2c22]], [[2c28\|2c28]], [[2c2e\|2c2e]], [[2c2r\|2c2r]]</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=2c2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c2d RCSB], [http://www.ebi.ac.uk/pdbsum/2c2d 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/c2/2c2d_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 ==
			DNA polymerases insert dATP opposite the oxidative damage product 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) instead of dCTP, to the extent of >90% with some polymerases. Steady-state kinetics with the Y-family Sulfolobus solfataricus DNA polymerase IV (Dpo4) showed 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) was similar for G and 8-oxoG templates. Mass spectral analysis of extended DNA primers showed >/=95% incorporation of dCTP > dATP opposite 8-oxoG. Pre-steady-state kinetics showed faster rates of dCTP incorporation opposite 8-oxoG than G. The measured K(d)(,dCTP) was 15-fold lower for an oligonucleotide containing 8-oxoG than with G. Extension beyond an 8-oxoG:C pair was similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. The E(a) for dCTP insertion opposite 8-oxoG was lower than for opposite G. Crystal structures of Dpo4 complexes with oligonucleotides were solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG. With ddCTP, dCTP, and dATP the phosphodiester bonds were formed even in the presence of Ca(2+). The 8-oxoG:C pair showed classic Watson-Crick geometry; the 8-oxoG:A pair was in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5' C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshift event observed in the catalytic assays.

	~~{{STRUCTURE_2c2d\| PDB=2c2d \| SCENE= }}~~		Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.,Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP J Biol Chem. 2006 Jan 27;281(4):2358-72. Epub 2005 Nov 22. PMID:16306039<ref>PMID:16306039</ref>

	~~===EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7~~,~~8-DIHYDRO-8-OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16306039}}~~

	~~==About this Structure==~~
	~~[[2c2d]] is~~ a ~~3 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2C2D OCA].~~

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016306039<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA at 15:56, 20 October 2012

2012-10-20T15:56:48Z

← Older revision		Revision as of 15:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2c2d]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA].		[[2c2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2D OCA].

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