2br0 - Revision history

OCA at 07:27, 3 November 2022

OCA — Thu, 03 Nov 2022 07:27:23 GMT

←Older revision		Revision as of 07:27, 3 November 2022
Line 3:		Line 3:
	<StructureSection load='2br0' size='340' side='right'caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='2br0' size='340' side='right'caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2br0]] is a 3 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BR0 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>~~</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=GNE:1,N2-ETHENOGUANINE'>GNE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</div></td></tr>	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPO4 ([https://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'>[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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [https://pdbe.org/2br0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [https://www.ebi.ac.uk/pdbsum/2br0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2br0 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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [https://pdbe.org/2br0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [https://www.ebi.ac.uk/pdbsum/2br0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2br0 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 2br0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2br0" 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: Egli M]]
-	[[Category: Irimia, A]]	+	[[Category: Irimia A]]
-	[[Category: Loukachevitch~~, L V]]~~	+	[[Category: Loukachevitch LV]]
-	~~[[Category: 1n2-ethenoguanine adduct]]~~	+
-	~~[[Category: Datp]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: P2 dna polymerase iv]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Translesion dna polymerase~~]]	+

OCA at 11:42, 3 February 2021

OCA — Wed, 03 Feb 2021 11:42:26 GMT

←Older revision		Revision as of 11:42, 3 February 2021
Line 1:		Line 1:

	==DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==		==DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==
-	<StructureSection load='2br0' size='340' side='right' caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>	+	<StructureSection load='2br0' size='340' side='right'caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BR0 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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 ([https://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'>[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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [~~http~~://pdbe.org/2br0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2br0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2br0 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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [https://pdbe.org/2br0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [https://www.ebi.ac.uk/pdbsum/2br0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2br0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</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 06:30, 16 May 2018

OCA — Wed, 16 May 2018 06:30:27 GMT

←Older revision		Revision as of 06:30, 16 May 2018
Line 1:		Line 1:
-	==DNA ~~ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4~~. ~~ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE~~-~~PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT~~ 1,N2-~~ETHENOGUANINE~~==	+
		+	==DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine==
	<StructureSection load='2br0' size='340' side='right' caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='2br0' size='340' side='right' caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 8:		Line 9:
	<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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://pdbe.org/2br0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://pdbe.org/2br0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2br0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/br/2br0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/br/2br0_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>
	</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=2br0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:14, 11 September 2015

OCA — Fri, 11 Sep 2015 09:14:40 GMT

←Older revision		Revision as of 09:14, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2br0' size='340' side='right' caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='2br0' size='340' side='right' caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BR0 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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=~~2287 Sulfolobus solfataricus~~])</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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://pdbe.org/2br0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	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 2br0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</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 09:20, 8 January 2015

OCA — Thu, 08 Jan 2015 09:20:16 GMT

←Older revision		Revision as of 09:20, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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=2287 Sulfolobus solfataricus])</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=2287 Sulfolobus solfataricus])</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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 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 37:		Line 37:
	[[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: 1n2-ethenoguanine adduct]]		[[Category: 1n2-ethenoguanine adduct]]
	[[Category: Datp]]		[[Category: Datp]]

OCA at 05:42, 29 September 2014

OCA — Mon, 29 Sep 2014 05:42:57 GMT

←Older revision		Revision as of 05:42, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2br0.~~png~~\|~~left~~\|200px]]	+	==DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1,N2-ETHENOGUANINE==
		+	<StructureSection load='2br0' size='340' side='right' caption='[[2br0]], [[Resolution\|resolution]] 2.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2br0]] 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=2BR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BR0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</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]], [[2bq3\|2bq3]], [[2bqr\|2bqr]], [[2bqu\|2bqu]]</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=2287 Sulfolobus solfataricus])</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=2br0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2br0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2br0 RCSB], [http://www.ebi.ac.uk/pdbsum/2br0 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/br/2br0_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 ==
		+	1,N(2)-Etheno(epsilon)guanine is a mutagenic DNA lesion derived from lipid oxidation products and also from some chemical carcinogens. Gel electrophoretic analysis of the products of primer extension by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) indicated preferential incorporation of A opposite 3'-(1,N(2)-epsilon-G)TACT-5', among the four dNTPs tested individually. With the template 3'-(1,N(2)-epsilon-G)CACT-5', both G and A were incorporated. When primer extension was done in the presence of a mixture of all four dNTPs, high pressure liquid chromatography-mass spectrometry analysis of the products indicated that (opposite 3'-(1,N(2)-epsilon-G)CACT-5') the major product was 5'-GTGA-3' and the minor product was 5'-AGTGA-3'. With the template 3'-(1,N(2)-epsilon-G)TACT-5', the following four products were identified by high pressure liquid chromatography-mass spectrometry: 5'-AATGA-3', 5'-ATTGA-3', 5'-ATGA-3', and 5'-TGA-3'. An x-ray crystal structure of Dpo4 was solved (2.1 A) with a primer-template and A placed in the primer to be opposite the 1,N(2)-epsilon-G in the template 3'-(1,N(2)-epsilon-G)TACT 5'. The added A in the primer was paired across the template T with classic Watson-Crick geometry. Similar structures were observed in a ternary Dpo4-DNA-dATP complex and a ternary Dpo4-DNA-ddATP complex, with d(d)ATP opposite the template T. A similar structure was observed with a ddGTP adjacent to the primer and opposite the C next to 1,N(2)-epsilon-G in 3'-(1,N(2)-epsilon-G)CACT-5'. We concluded that Dpo4 uses several mechanisms, including A incorporation opposite 1,N(2)-epsilon-G and also a variation of dNTP-stabilized misalignment, to generate both base pair and frameshift mutations.

-	~~{{STRUCTURE_2br0\| PDB=2br0 \| SCENE= }}~~	+	DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine.,Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP J Biol Chem. 2005 Aug 19;280(33):29750-64. Epub 2005 Jun 17. PMID:15965231<ref>PMID:15965231</ref>

-	~~===DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1~~,~~N2-ETHENOGUANINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15965231}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2br0]] 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=2BR0 OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015965231<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA at 17:45, 20 October 2012

OCA — Sat, 20 Oct 2012 17:45:45 GMT

←Older revision		Revision as of 17:45, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2br0]] 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=2BR0 OCA].	+	[[2br0]] 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=2BR0 OCA].

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

OCA: Protected "2br0" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 01:54:52 GMT

Protected "2br0" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:54, 27 July 2012

OCA at 01:54, 27 July 2012

OCA — Fri, 27 Jul 2012 01:54:50 GMT

←Older revision		Revision as of 01:54, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2br0.png\|left\|200px]]		[[Image:2br0.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2br0", 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_2br0\| PDB=2br0 \| SCENE= }}		{{STRUCTURE_2br0\| PDB=2br0 \| SCENE= }}

	===DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1,N2-ETHENOGUANINE===		===DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1,N2-ETHENOGUANINE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15965231}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15965231 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15965231}}		{{ABSTRACT_PUBMED_15965231}}

	==About this Structure==		==About this Structure==
-	~~2BR0~~ is a 3 ~~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=2BR0 OCA].	+	[[2br0]] 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=2BR0 OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15965231~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015965231</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
Line 35:		Line 26:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Translesion dna polymerase]]		[[Category: Translesion dna polymerase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:34:08 2009''

OCA at 16:34, 17 February 2009

OCA — Tue, 17 Feb 2009 16:34:09 GMT

←Older revision		Revision as of 16:34, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2BR0 is a ~~[[Single protein]]~~ structure of ~~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=2BR0 OCA].	+	2BR0 is a 3 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=2BR0 OCA].

	==Reference==		==Reference==
-	DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine., Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP, J Biol Chem. 2005 Aug 19;280(33):29750-64. Epub 2005 Jun 17. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15965231 15965231]~~	+	<ref group="xtra">PMID:15965231</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Single protein]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
	[[Category: Egli, M.]]		[[Category: Egli, M.]]
Line 37:		Line 36:
	[[Category: Translesion dna polymerase]]		[[Category: Translesion dna polymerase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:33:~~01 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:34:08 2009''