1s0o - Revision history

OCA at 06:10, 23 August 2023

OCA — Wed, 23 Aug 2023 06:10:56 GMT

←Older revision		Revision as of 06:10, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1s0o' size='340' side='right'caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1s0o' size='340' side='right'caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s0o]] is a 6 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=1S0O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1S0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s0o]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S0O 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=MG:MAGNESIUM+ION'>MG</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='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=273057 SULSO])</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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [https://pdbe.org/1s0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [https://www.ebi.ac.uk/pdbsum/1s0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s0o ProSAT]</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~~://proteopedia.org/fgij/fg.htm?mol=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [~~http~~://pdbe.org/1s0o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1s0o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1s0o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~DPO4_SULSO DPO4_SULSO]~~] 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.~~[HAMAP-Rule:MF_01113]~~	+	[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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sulso~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: Boudsocq, F]]	+	[[Category: Boudsocq F]]
-	[[Category: Ling, H]]	+	[[Category: Ling H]]
-	[[Category: Woodgate, R]]	+	[[Category: Woodgate R]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	~~[[Category: Abaic lesion]]~~	+
-	~~[[Category: Lesion bypass]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 13:37, 16 December 2020

OCA — Wed, 16 Dec 2020 13:37:33 GMT

←Older revision		Revision as of 13:37, 16 December 2020
Line 1:		Line 1:

	==Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift==		==Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift==
-	<StructureSection load='1s0o' size='340' side='right' caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1s0o' size='340' side='right'caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s0o]] is a 6 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=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1S0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s0o]] is a 6 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=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1S0O 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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">[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</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]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://pdbe.org/1s0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s0o ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://pdbe.org/1s0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s0o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Sulso]]		[[Category: Sulso]]
	[[Category: Boudsocq, F]]		[[Category: Boudsocq, F]]

OCA at 07:12, 8 March 2018

OCA — Thu, 08 Mar 2018 07:12:07 GMT

←Older revision		Revision as of 07:12, 8 March 2018
Line 1:		Line 1:
		+
	==Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift==		==Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift==
	<StructureSection load='1s0o' size='340' side='right' caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1s0o' size='340' side='right' caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://pdbe.org/1s0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o 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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://pdbe.org/1s0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s0o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s0/1s0o_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s0/1s0o_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 01:31, 8 February 2016

OCA — Mon, 08 Feb 2016 01:31:25 GMT

←Older revision		Revision as of 01:31, 8 February 2016
Line 19:		Line 19:
	<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=1s0o ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:37, 10 September 2015

OCA — Thu, 10 Sep 2015 06:37:26 GMT

←Older revision		Revision as of 06:37, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1s0o' size='340' side='right' caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1s0o' size='340' side='right' caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s0o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s0o]] is a 6 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=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S0O 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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">[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 ~~Sulfolobus solfataricus P2~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o 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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://pdbe.org/1s0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1s0o" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Sulfolobus solfataricus p2~~]]	+	[[Category: Sulso]]
	[[Category: Boudsocq, F]]		[[Category: Boudsocq, F]]
	[[Category: Ling, H]]		[[Category: Ling, H]]

OCA at 19:34, 24 December 2014

OCA — Wed, 24 Dec 2014 19:34:28 GMT

←Older revision		Revision as of 19:34, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s0o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S0O FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s0o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S0O 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 Sulfolobus solfataricus P2])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 Sulfolobus solfataricus P2])</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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o 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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] 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.[HAMAP-Rule:MF_01113]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus p2]]		[[Category: Sulfolobus solfataricus p2]]
-	[[Category: Boudsocq, F.]]	+	[[Category: Boudsocq, F]]
-	[[Category: Ling, H.]]	+	[[Category: Ling, H]]
-	[[Category: Woodgate, R.]]	+	[[Category: Woodgate, R]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
	[[Category: Abaic lesion]]		[[Category: Abaic lesion]]
	[[Category: Lesion bypass]]		[[Category: Lesion bypass]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 22:04, 28 September 2014

OCA — Sun, 28 Sep 2014 22:04:43 GMT

←Older revision		Revision as of 22:04, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1s0o.~~png~~\|~~left~~\|200px]]	+	==Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift==
		+	<StructureSection load='1s0o' size='340' side='right' caption='[[1s0o]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1s0o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S0O 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jx4\|1jx4]], [[1ryr\|1ryr]], [[1rys\|1rys]], [[1s0m\|1s0m]], [[1s0n\|1s0n]], [[1s10\|1s10]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 Sulfolobus solfataricus P2])</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=1s0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s0o RCSB], [http://www.ebi.ac.uk/pdbsum/1s0o 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/s0/1s0o_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 ==
		+	Dpo4 from S. Solfataricus, a DinB-like Y family polymerase, efficiently replicates DNA past an abasic lesion. We have determined crystal structures of Dpo4 complexed with five different abasic site-containing DNA substrates and find that translesion synthesis is template directed with the abasic site looped out and the incoming nucleotide is opposite the base 5' to the lesion. The ensuing DNA synthesis generates a -1 frameshift when the abasic site remains extrahelical. Template realignment during primer extension is also observed, resulting in base substitutions or even +1 frameshifts. In the case of a +1 frameshift, the extra nucleotide is accommodated in the solvent-exposed minor groove. In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis.

-	~~{{STRUCTURE_1s0o\| PDB=1s0o \| SCENE= }}~~	+	Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.,Ling H, Boudsocq F, Woodgate R, Yang W Mol Cell. 2004 Mar 12;13(5):751-62. PMID:15023344<ref>PMID:15023344</ref>

-	~~===Snapshots~~ of ~~replication through an abasic lesion: structural basis for base substitution and frameshift===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15023344}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1s0o]] is a 6 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=1S0O OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015023344<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Sulfolobus solfataricus]]	+	[[Category: Sulfolobus solfataricus p2]]
	[[Category: Boudsocq, F.]]		[[Category: Boudsocq, F.]]
	[[Category: Ling, H.]]		[[Category: Ling, H.]]

OCA at 08:27, 20 October 2012

OCA — Sat, 20 Oct 2012 08:27:26 GMT

←Older revision		Revision as of 08:27, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1s0o]] is a 6 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=1S0O OCA].	+	[[1s0o]] is a 6 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=1S0O OCA].

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

OCA: Protected "1s0o" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 19:36:06 GMT

Protected "1s0o" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:36, 25 July 2012

OCA at 19:36, 25 July 2012

OCA — Wed, 25 Jul 2012 19:36:04 GMT

←Older revision		Revision as of 19:36, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1s0o.png\|left\|200px]]		[[Image:1s0o.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1s0o", 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_1s0o\| PDB=1s0o \| SCENE= }}		{{STRUCTURE_1s0o\| PDB=1s0o \| SCENE= }}

	===Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift===		===Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15023344}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15023344 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15023344}}		{{ABSTRACT_PUBMED_15023344}}

	==About this Structure==		==About this Structure==
-	~~1S0O~~ is a 6 ~~chains~~ structure of ~~sequences~~ 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=1S0O OCA].	+	[[1s0o]] is a 6 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=1S0O OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15023344~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015023344</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
Line 33:		Line 24:
	[[Category: Lesion bypass]]		[[Category: Lesion bypass]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
-		+	[[Category: Transferase-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 17:50:10 2009''~~	+