2v4r - Revision history

OCA at 15:05, 13 December 2023

OCA — Wed, 13 Dec 2023 15:05:38 GMT

←Older revision		Revision as of 15:05, 13 December 2023
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	<StructureSection load='2v4r' size='340' side='right'caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2v4r' size='340' side='right'caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v4r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Sacs2 Sacs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V4R 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=DGT:~~2~~-DEOXYGUANOSINE-~~5~~-TRIPHOSPHATE'>DGT</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene~~></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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</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;'>[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [https://pdbe.org/2v4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [https://www.ebi.ac.uk/pdbsum/2v4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4r 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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [https://pdbe.org/2v4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [https://www.ebi.ac.uk/pdbsum/2v4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://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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	</div>		</div>
	<div class="pdbe-citations 2v4r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2v4r" 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: ~~Sacs2~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: Egli, M]]	+	[[Category: Synthetic construct]]
-	[[Category: Eoff~~, R L~~]]	+	[[Category: Egli M]]
-	[[Category: Guengerich~~, F P~~]]	+	[[Category: Eoff RL]]
-	[[Category: Marnett~~, L J~~]]	+	[[Category: Guengerich FP]]
-	[[Category: Rizzo~~, C J~~]]	+	[[Category: Marnett LJ]]
-	[[Category: Stafford~~, J B~~]]	+	[[Category: Rizzo CJ]]
-	[[Category: Szekely, J]]	+	[[Category: Stafford JB]]
-	~~[[Category: Cytoplasm]]~~	+	[[Category: Szekely J]]
-	~~[[Category: Dna adduct]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Dpo4]]~~	+
-	~~[[Category: M1dg]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mutator protein]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 20:57, 20 October 2021

OCA — Wed, 20 Oct 2021 20:57:23 GMT

←Older revision		Revision as of 20:57, 20 October 2021
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	<StructureSection load='2v4r' size='340' side='right'caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2v4r' size='340' side='right'caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v4r]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sacs2 Sacs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2V4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v4r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sacs2 Sacs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V4R 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [~~http~~://pdbe.org/2v4r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2v4r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4r 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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [https://pdbe.org/2v4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [https://www.ebi.ac.uk/pdbsum/2v4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4r 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_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]]
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	</div>		</div>
	<div class="pdbe-citations 2v4r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2v4r" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:10, 16 October 2019

OCA — Wed, 16 Oct 2019 06:10:59 GMT

←Older revision		Revision as of 06:10, 16 October 2019
Line 1:		Line 1:

	==Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine==		==Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine==
-	<StructureSection load='2v4r' size='340' side='right' caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2v4r' size='340' side='right'caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v4r]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sacs2 Sacs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>
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: ~~Sulso~~]]	+	[[Category: Large Structures]]
		+	[[Category: Sacs2]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Eoff, R L]]		[[Category: Eoff, R L]]

OCA at 08:08, 12 September 2018

OCA — Wed, 12 Sep 2018 08:08:28 GMT

←Older revision		Revision as of 08:08, 12 September 2018
Line 1:		Line 1:
-	==~~NON~~-~~PRODUCTIVE COMPLEX OF THE~~ Y-~~FAMILY~~ DNA ~~POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE~~==	+
		+	==Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine==
	<StructureSection load='2v4r' size='340' side='right' caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2v4r' size='340' side='right' caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://pdbe.org/2v4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r 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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://pdbe.org/2v4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4r 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/v4/2v4r_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v4/2v4r_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>
Line 46:		Line 47:
	[[Category: Stafford, J B]]		[[Category: Stafford, J B]]
	[[Category: Szekely, J]]		[[Category: Szekely, J]]
		+	[[Category: Cytoplasm]]
	[[Category: Dna adduct]]		[[Category: Dna adduct]]
	[[Category: Dna damage]]		[[Category: Dna damage]]

OCA at 17:47, 8 February 2016

OCA — Mon, 08 Feb 2016 17:47:41 GMT

←Older revision		Revision as of 17:47, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2v4r' size='340' side='right' caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2v4r' size='340' side='right' caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r 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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://pdbe.org/2v4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~DPO42_SULSO DPO42_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]	+	[[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 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=2v4r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2v4r" 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~~]]	+	[[Category: Sulso]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Eoff, R L]]		[[Category: Eoff, R L]]

OCA at 01:05, 25 December 2014

OCA — Thu, 25 Dec 2014 01:05:07 GMT

←Older revision		Revision as of 01:05, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r 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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO42_SULSO DPO42_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]]		[[Category: Sulfolobus solfataricus]]
-	[[Category: Egli, M.]]	+	[[Category: Egli, M]]
-	[[Category: Eoff, R L.]]	+	[[Category: Eoff, R L]]
-	[[Category: Guengerich, F P.]]	+	[[Category: Guengerich, F P]]
-	[[Category: Marnett, L J.]]	+	[[Category: Marnett, L J]]
-	[[Category: Rizzo, C J.]]	+	[[Category: Rizzo, C J]]
-	[[Category: Stafford, J B.]]	+	[[Category: Stafford, J B]]
-	[[Category: Szekely, J.]]	+	[[Category: Szekely, J]]
	[[Category: Dna adduct]]		[[Category: Dna adduct]]
	[[Category: Dna damage]]		[[Category: Dna damage]]

OCA at 07:15, 29 September 2014

OCA — Mon, 29 Sep 2014 07:15:44 GMT

←Older revision		Revision as of 07:15, 29 September 2014
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-	[[~~Image:~~2v4r.~~png~~\|~~left~~\|200px]]	+	==NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE==
		+	<StructureSection load='2v4r' size='340' side='right' caption='[[2v4r]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2v4r]] 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=2V4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V4R 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1G:3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5-MONOPHOSPHATE'>M1G</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2asl\|2asl]], [[1s0m\|1s0m]], [[2jeg\|2jeg]], [[1rys\|1rys]], [[2j6t\|2j6t]], [[1n56\|1n56]], [[2atl\|2atl]], [[1jx4\|1jx4]], [[2c22\|2c22]], [[2va2\|2va2]], [[1s97\|1s97]], [[2agq\|2agq]], [[2jej\|2jej]], [[2ago\|2ago]], [[2asj\|2asj]], [[2asd\|2asd]], [[1n48\|1n48]], [[1jxl\|1jxl]], [[2bq3\|2bq3]], [[2j6u\|2j6u]], [[2uvu\|2uvu]], [[2agp\|2agp]], [[2c2r\|2c2r]], [[1s0n\|1s0n]], [[1s0o\|1s0o]], [[2jef\|2jef]], [[2uvw\|2uvw]], [[2bqr\|2bqr]], [[2jei\|2jei]], [[2bqu\|2bqu]], [[1s9f\|1s9f]], [[2au0\|2au0]], [[2c28\|2c28]], [[2v9w\|2v9w]], [[2c2e\|2c2e]], [[1ryr\|1ryr]], [[2c2d\|2c2d]], [[2uvv\|2uvv]], [[1s10\|1s10]], [[2br0\|2br0]], [[2j6s\|2j6s]], [[2uvr\|2uvr]], [[2va3\|2va3]], [[2v4q\|2v4q]], [[2v4s\|2v4s]], [[2v4t\|2v4t]]</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=2v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v4r RCSB], [http://www.ebi.ac.uk/pdbsum/2v4r 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/v4/2v4r_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 ==
		+	Oxidative stress can induce the formation of reactive electrophiles, such as DNA peroxidation products, e.g. base propenals, and lipid peroxidation products, e.g. malondialdehyde. Base propenals and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-ss-D-erythro-pentofuranosyl)-pyrimido[1,2-alpha]purin-10(3H)-o ne (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG (N2-OPdG). Previous work has shown that M1dG is mutagenic in bacteria and mammalian cells and that its mutagenicity in Escherichia coli is dependent on induction of the SOS response, indicating a role for translesion DNA polymerases in the bypass of M1dG. To probe the mechanism by which translesion polymerases bypass M1dG, kinetic and structural studies were conducted with a model Y-family DNA polymerase, Dpo4 from Sulfolobus solfataricus. Steady-state incorporation of dNTPs opposite M1dG was reduced 260- to 2,900-fold and exhibited a preference for dATP incorporation. LC-MS/MS analysis of the full-length extension products revealed a spectrum of products arising principally by incorporation of dC or dA opposite M1dG followed by partial or full-length extension. A greater proportion of -1 deletions were observed when dT was positioned 5' of M1dG. Two crystal structures were solved, including a "Type II" frameshift deletion complex and another complex with Dpo4 bound to a dC:M1dG pair located in the post-insertion context. Importantly, M1dG was in the ring-closed state in both structures and in the structure with dC opposite M1dG, the dC residue moved out of the Dpo4 active site, into the minor groove. The results are consistent with the reported mutagenicity of M1dG and illustrate how the lesion may affect replication events.

-	~~{{STRUCTURE_2v4r\| PDB=2v4r \| SCENE= }}~~	+	Structural and Functional Analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed Bypass of the Malondialdehyde-deoxyguanosine Adduct.,Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ Biochemistry. 2009 Jun 4. PMID:19492857<ref>PMID:19492857</ref>

-	~~===NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19492857}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2v4r]] 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=2V4R OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019492857<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA at 10:57, 20 October 2012

OCA — Sat, 20 Oct 2012 10:57:09 GMT

←Older revision		Revision as of 10:57, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2v4r]] 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=2V4R OCA].	+	[[2v4r]] 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=2V4R OCA].

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

OCA at 03:47, 26 July 2012

OCA — Thu, 26 Jul 2012 03:47:54 GMT

←Older revision		Revision as of 03:47, 26 July 2012
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	[[Image:2v4r.png\|left\|200px]]		[[Image:2v4r.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2v4r\| PDB=2v4r \| SCENE= }}		{{STRUCTURE_2v4r\| PDB=2v4r \| SCENE= }}

	===NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE===		===NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE===

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

	==Reference==		==Reference==
Line 35:		Line 24:
	[[Category: Stafford, J B.]]		[[Category: Stafford, J B.]]
	[[Category: Szekely, J.]]		[[Category: Szekely, J.]]
		+	[[Category: Dna adduct]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna replication]]
		+	[[Category: Dna-binding]]
		+	[[Category: Dna-directed dna polymerase]]
		+	[[Category: Dpo4]]
		+	[[Category: M1dg]]
		+	[[Category: Magnesium]]
		+	[[Category: Metal-binding]]
		+	[[Category: Mutator protein]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Transferase]]

OCA: Protected "2v4r" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2011 04:45:00 GMT

Protected "2v4r" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:45, 1 June 2011