3k5n - Revision history

OCA at 10:15, 21 February 2024

OCA — Wed, 21 Feb 2024 10:15:13 GMT

←Older revision		Revision as of 10:15, 21 February 2024
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	<StructureSection load='3k5n' size='340' side='right'caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='3k5n' size='340' side='right'caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K5N FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</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]] 3.15Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3k57\|3k57]]~~, [[~~3k58~~\|~~3k58~~]]~~, [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>b0060, dinA, JW0059, polB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [https://pdbe.org/3k5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [https://www.ebi.ac.uk/pdbsum/3k5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k5n 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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [https://pdbe.org/3k5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [https://www.ebi.ac.uk/pdbsum/3k5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k5n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPO2_ECOLI DPO2_ECOLI]] Thought to be involved in DNA repair and/or mutagenesis.	+	[https://www.uniprot.org/uniprot/DPO2_ECOLI DPO2_ECOLI] Thought to be involved in DNA repair and/or mutagenesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3k5n 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=3k5n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	E. coli DNA Pol II and eukaryotic Rev3 are B-family polymerases that can extend primers past a damaged or mismatched site when the high-fidelity replicative polymerases in the same family are ineffective. We report here the biochemical and structural properties of DNA Pol II that facilitate this translesion synthesis. DNA Pol II can extend primers past lesions either directly or by template skipping, in which small protein cavities outside of the active site accommodate looped-out template nucleotides 1 or 2 bp upstream. Because of multiple looping-out alternatives, mutation spectra of bypass synthesis are complicated. Moreover, translesion synthesis is enhanced by altered partitioning of DNA substrate between the polymerase active site and the proofreading exonuclease site. Compared to the replicative B family polymerases, DNA Pol II has subtle amino acid changes remote from the active site that allow it to replicate normal DNA with high efficiency yet conduct translesion synthesis when needed.

-	~~Structural insight into translesion synthesis by DNA Pol II.,Wang F, Yang W Cell. 2009 Dec 24;139(7):1279-89. PMID:20064374<ref>PMID:20064374</ref>~~	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 3k5n" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wang, F]]	+	[[Category: Wang F]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Sos response]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 12:21, 13 October 2021

OCA — Wed, 13 Oct 2021 12:21:55 GMT

←Older revision		Revision as of 12:21, 13 October 2021
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	==Crystal structure of E.coli Pol II-abasic DNA binary complex==		==Crystal structure of E.coli Pol II-abasic DNA binary complex==
-	<StructureSection load='3k5n' size='340' side='right' caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='3k5n' size='340' side='right'caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3K5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K5N FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [~~http~~://pdbe.org/3k5n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3k5n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3k5n 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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [https://pdbe.org/3k5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [https://www.ebi.ac.uk/pdbsum/3k5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k5n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPO2_ECOLI DPO2_ECOLI]] Thought to be involved in DNA repair and/or mutagenesis.	+	[[https://www.uniprot.org/uniprot/DPO2_ECOLI DPO2_ECOLI]] Thought to be involved in DNA repair and/or mutagenesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Wang, F]]		[[Category: Wang, F]]
	[[Category: Yang, W]]		[[Category: Yang, W]]

OCA at 08:59, 26 December 2018

OCA — Wed, 26 Dec 2018 08:59:08 GMT

←Older revision		Revision as of 08:59, 26 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of E.coli Pol II-abasic DNA binary complex==		==Crystal structure of E.coli Pol II-abasic DNA binary complex==
	<StructureSection load='3k5n' size='340' side='right' caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='3k5n' size='340' side='right' caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://pdbe.org/3k5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n 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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://pdbe.org/3k5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k5n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/3k5n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/3k5n_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 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3k5n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3k5n" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:38, 9 February 2016

OCA — Tue, 09 Feb 2016 21:38:10 GMT

←Older revision		Revision as of 21:38, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3k5n' size='340' side='right' caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='3k5n' size='340' side='right' caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K5N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K5N FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n 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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://pdbe.org/3k5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3k5n 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 3k5n" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Escherichia coli]]
	[[Category: Wang, F]]		[[Category: Wang, F]]
	[[Category: Yang, W]]		[[Category: Yang, W]]

OCA at 09:42, 25 December 2014

OCA — Thu, 25 Dec 2014 09:42:37 GMT

←Older revision		Revision as of 09:42, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K5N FirstGlance]. <br>		<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K5N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n 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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO2_ECOLI DPO2_ECOLI]] Thought to be involved in DNA repair and/or mutagenesis.
	== 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: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Wang, F.]]	+	[[Category: Wang, F]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Dna repair]]		[[Category: Dna repair]]

OCA at 12:46, 29 September 2014

OCA — Mon, 29 Sep 2014 12:46:23 GMT

←Older revision		Revision as of 12:46, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3k5n.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of E.coli Pol II-abasic DNA binary complex==
		+	<StructureSection load='3k5n' size='340' side='right' caption='[[3k5n]], [[Resolution\|resolution]] 3.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3k5n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K5N FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3k57\|3k57]], [[3k58\|3k58]], [[3k59\|3k59]], [[3k5a\|3k5a]], [[3k5l\|3k5l]], [[3k5m\|3k5m]], [[3k5o\|3k5o]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0060, dinA, JW0059, polB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3k5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k5n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k5n RCSB], [http://www.ebi.ac.uk/pdbsum/3k5n 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/k5/3k5n_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 ==
		+	E. coli DNA Pol II and eukaryotic Rev3 are B-family polymerases that can extend primers past a damaged or mismatched site when the high-fidelity replicative polymerases in the same family are ineffective. We report here the biochemical and structural properties of DNA Pol II that facilitate this translesion synthesis. DNA Pol II can extend primers past lesions either directly or by template skipping, in which small protein cavities outside of the active site accommodate looped-out template nucleotides 1 or 2 bp upstream. Because of multiple looping-out alternatives, mutation spectra of bypass synthesis are complicated. Moreover, translesion synthesis is enhanced by altered partitioning of DNA substrate between the polymerase active site and the proofreading exonuclease site. Compared to the replicative B family polymerases, DNA Pol II has subtle amino acid changes remote from the active site that allow it to replicate normal DNA with high efficiency yet conduct translesion synthesis when needed.

-	~~{{STRUCTURE_3k5n\| PDB=3k5n \| SCENE= }}~~	+	Structural insight into translesion synthesis by DNA Pol II.,Wang F, Yang W Cell. 2009 Dec 24;139(7):1279-89. PMID:20064374<ref>PMID:20064374</ref>

-	~~===Crystal structure~~ of E.~~coli Pol II-abasic DNA binary complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20064374}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3k5n]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020064374<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 15:13, 20 October 2012

OCA — Sat, 20 Oct 2012 15:13:51 GMT

←Older revision		Revision as of 15:13, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3k5n]] is a 4 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA].	+	[[3k5n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA].

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

OCA: Protected "3k5n" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 17:42:57 GMT

Protected "3k5n" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:42, 26 July 2012

OCA at 17:42, 26 July 2012

OCA — Thu, 26 Jul 2012 17:42:55 GMT

←Older revision		Revision as of 17:42, 26 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3k5n.png\|left\|200px]]
-	[[Image:3k5n.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3k5n", 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_3k5n\| PDB=3k5n \| SCENE= }}		{{STRUCTURE_3k5n\| PDB=3k5n \| SCENE= }}

	===Crystal structure of E.coli Pol II-abasic DNA binary complex===		===Crystal structure of E.coli Pol II-abasic DNA binary complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20064374}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20064374 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20064374}}		{{ABSTRACT_PUBMED_20064374}}

	==About this Structure==		==About this Structure==
-	~~3K5N~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA].	+	[[3k5n]] is a 4 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20064374~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020064374</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 35:		Line 26:
	[[Category: Sos response]]		[[Category: Sos response]]
	[[Category: Transferase]]		[[Category: Transferase]]
-		+	[[Category: Transferase-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 3 09:37:04 2010''~~	+

OCA at 07:37, 3 February 2010

OCA — Wed, 03 Feb 2010 07:37:05 GMT

←Older revision		Revision as of 07:37, 3 February 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3k5n.jpg\|left\|200px]]

-	The ~~entry 3k5n~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3k5n", 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_3k5n\| PDB=3k5n \| SCENE= }}

-	~~Authors: Yang, W., Wang, F~~.	+	===Crystal structure of E.coli Pol II-abasic DNA binary complex===

-	Description: Crystal structure of E.coli Pol II-abasic DNA binary complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 30 13~~:46:~~25 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20064374}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20064374 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20064374}}
		+
		+	==About this Structure==
		+	3K5N is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K5N OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20064374</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Wang, F.]]
		+	[[Category: Yang, W.]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna-binding]]
		+	[[Category: Dna-directed dna polymerase]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Sos response]]
		+	[[Category: Transferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:37:04 2010''