3pzp - Revision history

OCA at 13:35, 1 March 2024

OCA — Fri, 01 Mar 2024 13:35:53 GMT

←Older revision		Revision as of 13:35, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3pzp' size='340' side='right'caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>		<StructureSection load='3pzp' size='340' side='right'caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PZP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DTP:2~~-~~DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.336Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~TTD~~:~~CIS~~-~~SYN~~+~~CYCLOBUTANE+THYMINE+DIMER~~'>~~TTD~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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;~~'>~~[[1t94\|1t94]], [[2oh2\|2oh2]], [[3in5\|3in5]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLK~~, ~~DINB1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~<~~/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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [https://pdbe.org/3pzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [https://www.ebi.ac.uk/pdbsum/3pzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pzp 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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [https://pdbe.org/3pzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [https://www.ebi.ac.uk/pdbsum/3pzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pzp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>	+	[https://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase kappa (Polkappa), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Polkappa in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Polkappa in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.	+

-	Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.,Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson RE, Prakash L, Prakash S, Aggarwal AK J Mol Biol. 2011 Apr 29;408(2):252-61. Epub 2011 Feb 24. PMID:21354175<ref>PMID:21354175</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 3pzp" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aggarwal~~, A K]]~~	+	[[Category: Aggarwal AK]]
-	~~[[Category: Carpio, R Vasquez-Del~~]]	+	[[Category: Johnson RE]]
-	[[Category: Johnson~~, R E~~]]	+	[[Category: Lone S]]
-	[[Category: Lone, S]]	+	[[Category: Prakash L]]
-	[[Category: Prakash, L]]	+	[[Category: Prakash S]]
-	[[Category: Prakash, S]]	+	[[Category: Silverstein TD]]
-	[[Category: Silverstein~~, T D~~]]	+	[[Category: Vasquez-Del Carpio R]]
-	[[Category: ~~Dna binding nucleotide binding magnesium binding]]~~	+
-	~~[[Category: Dna nucleotidyltransferase]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Transferase~~-~~dna complex~~]]	+

OCA at 09:03, 25 May 2022

OCA — Wed, 25 May 2022 09:03:14 GMT

←Older revision		Revision as of 09:03, 25 May 2022
Line 1:		Line 1:

	==Human DNA polymerase kappa extending opposite a cis-syn thymine dimer==		==Human DNA polymerase kappa extending opposite a cis-syn thymine dimer==
-	<StructureSection load='3pzp' size='340' side='right' caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>	+	<StructureSection load='3pzp' size='340' side='right'caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PZP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t94\|1t94]], [[2oh2\|2oh2]], [[3in5\|3in5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t94\|1t94]], [[2oh2\|2oh2]], [[3in5\|3in5]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLK, DINB1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLK, DINB1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [~~http~~://pdbe.org/3pzp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pzp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pzp 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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [https://pdbe.org/3pzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [https://www.ebi.ac.uk/pdbsum/3pzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pzp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>	+	[[https://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 3pzp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pzp" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 28:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Aggarwal, A K]]		[[Category: Aggarwal, A K]]
	[[Category: Carpio, R Vasquez-Del]]		[[Category: Carpio, R Vasquez-Del]]

OCA at 13:29, 5 August 2016

OCA — Fri, 05 Aug 2016 13:29:58 GMT

←Older revision		Revision as of 13:29, 5 August 2016
Line 1:		Line 1:
		+
	==Human DNA polymerase kappa extending opposite a cis-syn thymine dimer==		==Human DNA polymerase kappa extending opposite a cis-syn thymine dimer==
	<StructureSection load='3pzp' size='340' side='right' caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>		<StructureSection load='3pzp' size='340' side='right' caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PZP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t94\|1t94]], [[2oh2\|2oh2]], [[3in5\|3in5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t94\|1t94]], [[2oh2\|2oh2]], [[3in5\|3in5]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLK, DINB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLK, DINB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [http://www.ebi.ac.uk/pdbsum/3pzp 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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [http://pdbe.org/3pzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [http://www.ebi.ac.uk/pdbsum/3pzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pzp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 3pzp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Aggarwal, A K]]		[[Category: Aggarwal, A K]]
	[[Category: Carpio, R Vasquez-Del]]		[[Category: Carpio, R Vasquez-Del]]

OCA at 02:53, 25 December 2014

OCA — Thu, 25 Dec 2014 02:53:02 GMT

←Older revision		Revision as of 02:53, 25 December 2014
Line 10:		Line 10:
	<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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [http://www.ebi.ac.uk/pdbsum/3pzp 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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [http://www.ebi.ac.uk/pdbsum/3pzp PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLK_HUMAN POLK_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.<ref>PMID:10620008</ref> <ref>PMID:11024016</ref> <ref>PMID:12145297</ref> <ref>PMID:12444249</ref> <ref>PMID:12952891</ref> <ref>PMID:14630940</ref> <ref>PMID:15533436</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:22, 9 December 2014

OCA — Tue, 09 Dec 2014 11:22:59 GMT

←Older revision		Revision as of 11:22, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3pzp.~~png~~\|~~left~~\|~~200px~~]]	+	==Human DNA polymerase kappa extending opposite a cis-syn thymine dimer==
		+	<StructureSection load='3pzp' size='340' side='right' caption='[[3pzp]], [[Resolution\|resolution]] 3.34Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PZP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t94\|1t94]], [[2oh2\|2oh2]], [[3in5\|3in5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLK, DINB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3pzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pzp RCSB], [http://www.ebi.ac.uk/pdbsum/3pzp PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase kappa (Polkappa), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Polkappa in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Polkappa in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

-	~~{{STRUCTURE_3pzp\| PDB=3pzp \| SCENE= }}~~	+	Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.,Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson RE, Prakash L, Prakash S, Aggarwal AK J Mol Biol. 2011 Apr 29;408(2):252-61. Epub 2011 Feb 24. PMID:21354175<ref>PMID:21354175</ref>

-	~~===Human DNA polymerase kappa extending opposite~~ a ~~cis-syn thymine dimer===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21354175}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3pzp]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021354175<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Aggarwal, A K.]]	+	[[Category: Aggarwal, A K]]
-	[[Category: Carpio, R Vasquez-Del.]]	+	[[Category: Carpio, R Vasquez-Del]]
-	[[Category: Johnson, R E.]]	+	[[Category: Johnson, R E]]
-	[[Category: Lone, S.]]	+	[[Category: Lone, S]]
-	[[Category: Prakash, L.]]	+	[[Category: Prakash, L]]
-	[[Category: Prakash, S.]]	+	[[Category: Prakash, S]]
-	[[Category: Silverstein, T D.]]	+	[[Category: Silverstein, T D]]
	[[Category: Dna binding nucleotide binding magnesium binding]]		[[Category: Dna binding nucleotide binding magnesium binding]]
	[[Category: Dna nucleotidyltransferase]]		[[Category: Dna nucleotidyltransferase]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 11:50, 20 October 2012

OCA — Sat, 20 Oct 2012 11:50:17 GMT

←Older revision		Revision as of 11:50, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3pzp]] is a 6 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA].	+	[[3pzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA].

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

OCA at 06:45, 26 July 2012

OCA — Thu, 26 Jul 2012 06:45:36 GMT

←Older revision		Revision as of 06:45, 26 July 2012
Line 1:		Line 1:
-	[[Image:3pzp.~~jpg~~\|left\|200px]]	+	[[Image:3pzp.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3pzp", 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_3pzp\| PDB=3pzp \| SCENE= }}		{{STRUCTURE_3pzp\| PDB=3pzp \| SCENE= }}

	===Human DNA polymerase kappa extending opposite a cis-syn thymine dimer===		===Human DNA polymerase kappa extending opposite a cis-syn thymine dimer===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21354175}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21354175 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21354175}}		{{ABSTRACT_PUBMED_21354175}}

	==About this Structure==		==About this Structure==
-	[[3pzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA].	+	[[3pzp]] is a 6 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==

OCA at 07:27, 28 December 2011

OCA — Wed, 28 Dec 2011 07:27:40 GMT

←Older revision		Revision as of 07:27, 28 December 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3pzp.jpg\|left\|200px]]

-	The ~~entry 3pzp~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3pzp", 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_3pzp\| PDB=3pzp \| SCENE= }}

-	~~Authors: Vasquez~~-~~Del Carpio, R., Silverstein, T.D., Lone, S., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.~~	+	===Human DNA polymerase kappa extending opposite a cis-syn thymine dimer===

-	~~Description~~: ~~Human~~ DNA polymerase ~~kappa extending opposite a cis~~-~~syn thymine dimer~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21354175}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21354175 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21354175}}
		+
		+	==About this Structure==
		+	[[3pzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PZP OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021354175</ref><references group="xtra"/>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Aggarwal, A K.]]
		+	[[Category: Carpio, R Vasquez-Del.]]
		+	[[Category: Johnson, R E.]]
		+	[[Category: Lone, S.]]
		+	[[Category: Prakash, L.]]
		+	[[Category: Prakash, S.]]
		+	[[Category: Silverstein, T D.]]
		+	[[Category: Dna binding nucleotide binding magnesium binding]]
		+	[[Category: Dna nucleotidyltransferase]]
		+	[[Category: Nucleus]]
		+	[[Category: Transferase-dna complex]]

OCA at 09:36, 23 February 2011

OCA — Wed, 23 Feb 2011 09:36:03 GMT

←Older revision		Revision as of 09:36, 23 February 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3pzp is ON HOLD	+	The entry 3pzp is ON HOLD until Paper Publication

	Authors: Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.		Authors: Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.

	Description: Human DNA polymerase kappa extending opposite a cis-syn thymine dimer		Description: Human DNA polymerase kappa extending opposite a cis-syn thymine dimer

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

OCA — Wed, 29 Dec 2010 18:16:20 GMT

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

←Older revision

Revision as of 18:16, 29 December 2010