2zvk - Revision history

OCA at 13:56, 1 November 2023

OCA — Wed, 01 Nov 2023 13:56:49 GMT

←Older revision		Revision as of 13:56, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zvk' size='340' side='right'caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2zvk' size='340' side='right'caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2zvl\|2zvl]], [[2zvm\|2zvm]]</div></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]] 2.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PCNA ([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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [https://pdbe.org/2zvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [https://www.ebi.ac.uk/pdbsum/2zvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvk 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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [https://pdbe.org/2zvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [https://www.ebi.ac.uk/pdbsum/2zvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PCNA_HUMAN PCNA_HUMAN]] Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.<ref>PMID:19443450</ref> <ref>PMID:18719106</ref>	+	[https://www.uniprot.org/uniprot/PCNA_HUMAN PCNA_HUMAN] Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.<ref>PMID:19443450</ref> <ref>PMID:18719106</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hanafusa, T]]	+	[[Category: Hanafusa T]]
-	[[Category: Hashimoto, H]]	+	[[Category: Hashimoto H]]
-	[[Category: Hishiki, A]]	+	[[Category: Hishiki A]]
-	[[Category: Kamei, K]]	+	[[Category: Kamei K]]
-	[[Category: Ohashi, E]]	+	[[Category: Ohashi E]]
-	[[Category: Ohmori, H]]	+	[[Category: Ohmori H]]
-	[[Category: Sato, M]]	+	[[Category: Sato M]]
-	[[Category: Shimizu, T]]	+	[[Category: Shimizu T]]
-	~~[[Category: Clamp]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Disease mutation]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Dna polymerase eta]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mutator protein]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Pcna]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Pip-box]]~~	+
-	~~[[Category: Schiff base]]~~	+
-	~~[[Category: Systemic lupus erythematosus]]~~	+
-	~~[[Category: Tl]]~~	+
-	~~[[Category: Tls polymerase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Translesion synthesis]]~~	+
-	~~[[Category: Xeroderma pigmentosum~~]]	+

OCA at 17:38, 15 December 2021

OCA — Wed, 15 Dec 2021 17:38:51 GMT

←Older revision		Revision as of 17:38, 15 December 2021
Line 1:		Line 1:

	==Crystal structure of PCNA in complex with DNA polymerase eta fragment==		==Crystal structure of PCNA in complex with DNA polymerase eta fragment==
-	<StructureSection load='2zvk' size='340' side='right' caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2zvk' size='340' side='right'caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zvl\|2zvl]], [[2zvm\|2zvm]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zvl\|2zvl]], [[2zvm\|2zvm]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PCNA ([~~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">PCNA ([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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [~~http~~://pdbe.org/2zvk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zvk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvk 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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [https://pdbe.org/2zvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [https://www.ebi.ac.uk/pdbsum/2zvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PCNA_HUMAN PCNA_HUMAN]] Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.<ref>PMID:19443450</ref> <ref>PMID:18719106</ref>	+	[[https://www.uniprot.org/uniprot/PCNA_HUMAN PCNA_HUMAN]] Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.<ref>PMID:19443450</ref> <ref>PMID:18719106</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Proliferating ~~Cell Nuclear Antigen~~\|Proliferating ~~Cell Nuclear Antigen~~]]	+	*[[Proliferating cell nuclear antigen 3D structures\|Proliferating cell nuclear antigen 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Hanafusa, T]]		[[Category: Hanafusa, T]]
	[[Category: Hashimoto, H]]		[[Category: Hashimoto, H]]

OCA at 06:58, 18 October 2018

OCA — Thu, 18 Oct 2018 06:58:35 GMT

←Older revision		Revision as of 06:58, 18 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of PCNA in complex with DNA polymerase eta fragment==		==Crystal structure of PCNA in complex with DNA polymerase eta fragment==
	<StructureSection load='2zvk' size='340' side='right' caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2zvk' size='340' side='right' caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PCNA ([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">PCNA ([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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://pdbe.org/2zvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk 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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://pdbe.org/2zvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zv/2zvk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zv/2zvk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 04:22, 10 February 2016

OCA — Wed, 10 Feb 2016 04:22:52 GMT

←Older revision		Revision as of 04:22, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='2zvk' size='340' side='right' caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2zvk' size='340' side='right' caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zvl\|2zvl]], [[2zvm\|2zvm]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zvl\|2zvl]], [[2zvm\|2zvm]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PCNA ([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">PCNA ([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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk 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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://pdbe.org/2zvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2zvk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2zvk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Hanafusa, T]]		[[Category: Hanafusa, T]]
	[[Category: Hashimoto, H]]		[[Category: Hashimoto, H]]

OCA at 11:46, 25 December 2014

OCA — Thu, 25 Dec 2014 11:46:05 GMT

←Older revision		Revision as of 11:46, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zvl\|2zvl]], [[2zvm\|2zvm]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zvl\|2zvl]], [[2zvm\|2zvm]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PCNA ([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">PCNA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk 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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCNA_HUMAN PCNA_HUMAN]] Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.<ref>PMID:19443450</ref> <ref>PMID:18719106</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Hanafusa, T.]]	+	[[Category: Hanafusa, T]]
-	[[Category: Hashimoto, H.]]	+	[[Category: Hashimoto, H]]
-	[[Category: Hishiki, A.]]	+	[[Category: Hishiki, A]]
-	[[Category: Kamei, K.]]	+	[[Category: Kamei, K]]
-	[[Category: Ohashi, E.]]	+	[[Category: Ohashi, E]]
-	[[Category: Ohmori, H.]]	+	[[Category: Ohmori, H]]
-	[[Category: Sato, M.]]	+	[[Category: Sato, M]]
-	[[Category: Shimizu, T.]]	+	[[Category: Shimizu, T]]
	[[Category: Clamp]]		[[Category: Clamp]]
	[[Category: Complex]]		[[Category: Complex]]

OCA at 07:31, 29 September 2014

OCA — Mon, 29 Sep 2014 07:31:38 GMT

←Older revision		Revision as of 07:31, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2zvk.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of PCNA in complex with DNA polymerase eta fragment==
		+	<StructureSection load='2zvk' size='340' side='right' caption='[[2zvk]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zvk]] 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=2ZVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zvl\|2zvl]], [[2zvm\|2zvm]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PCNA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2zvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvk RCSB], [http://www.ebi.ac.uk/pdbsum/2zvk 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/zv/2zvk_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 ==
		+	Translesion synthesis (TLS) is a DNA damage tolerance mechanism that allows continued DNA synthesis, even in the presence of damaged DNA templates. Mammals have multiple DNA polymerases specialized for TLS, including Poleta, Poliota, and Polkappa. These enzymes show preferential bypass for different lesions. Proliferating cell nuclear antigen (PCNA), which functions as a sliding clamp for the replicative polymerase Poldelta, also interacts with the three TLS polymerases. Although many PCNA-binding proteins have a highly conserved sequence termed the PCNA-interacting protein box (PIP-box), Poleta, Poliota, and Polkappa have a noncanonical PIP-box sequence. In response to DNA damage, Lys-164 of PCNA undergoes ubiquitination by the RAD6-RAD18 complex, and the ubiquitination is considered to facilitate TLS. Consistent with this, these three TLS polymerases have one or two ubiquitin binding domains and are recruited to replication forks via interactions with ubiquitinated PCNA involving the noncanonical PIP-box and ubiquitin binding domain. However, it is unclear how these TLS polymerases interact with PCNA. To address the structural basis for interactions between different TLS polymerases and PCNA, we determined crystal structures of PCNA bound to peptides containing the noncanonical PIP-box of these polymerases. We show that the three PIP-box peptides interact with PCNA in different ways, both from one another and from canonical PIP-box peptides. Especially, the PIP-box of Poliota adopts a novel structure. Furthermore, these structures enable us to speculate how these TLS polymerases interact with Lys-164-monoubiquitinated PCNA. Our results will provide clues to understanding the mechanism of preferential recruitment of TLS polymerases to the stalled forks.

-	~~{{STRUCTURE_2zvk\| PDB=2zvk \| SCENE= }}~~	+	Structural basis for novel interactions between human translesion synthesis polymerases and proliferating cell nuclear antigen.,Hishiki A, Hashimoto H, Hanafusa T, Kamei K, Ohashi E, Shimizu T, Ohmori H, Sato M J Biol Chem. 2009 Apr 17;284(16):10552-60. Epub 2009 Feb 10. PMID:19208623<ref>PMID:19208623</ref>

-	~~===Crystal structure~~ of ~~PCNA in complex with DNA polymerase eta fragment===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19208623}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2zvk]] 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=2ZVK OCA].~~	+

	==See Also==		==See Also==
	*[[Proliferating Cell Nuclear Antigen\|Proliferating Cell Nuclear Antigen]]		*[[Proliferating Cell Nuclear Antigen\|Proliferating Cell Nuclear Antigen]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019208623<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 16:19, 20 October 2012

OCA — Sat, 20 Oct 2012 16:19:02 GMT

←Older revision		Revision as of 16:19, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zvk]] is a 6 chain structure ~~of [[Proliferating Cell Nuclear Antigen]]~~ 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=2ZVK OCA].	+	[[2zvk]] 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=2ZVK OCA].

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

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

OCA — Thu, 26 Jul 2012 21:16:40 GMT

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

←Older revision

Revision as of 21:16, 26 July 2012

OCA at 21:16, 26 July 2012

OCA — Thu, 26 Jul 2012 21:16:38 GMT

←Older revision		Revision as of 21:16, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2zvk.png\|left\|200px]]		[[Image:2zvk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zvk", 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_2zvk\| PDB=2zvk \| SCENE= }}		{{STRUCTURE_2zvk\| PDB=2zvk \| SCENE= }}

	===Crystal structure of PCNA in complex with DNA polymerase eta fragment===		===Crystal structure of PCNA in complex with DNA polymerase eta fragment===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19208623}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19208623 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19208623}}		{{ABSTRACT_PUBMED_19208623}}

	==About this Structure==		==About this Structure==
-	~~2ZVK~~ is a 6 ~~chains~~ structure of ~~sequences~~ 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=2ZVK OCA].	+	[[2zvk]] is a 6 chain structure of [[Proliferating Cell Nuclear Antigen]] 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=2ZVK OCA].
		+
		+	==See Also==
		+	*[[Proliferating Cell Nuclear Antigen\|Proliferating Cell Nuclear Antigen]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19208623~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019208623</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 34:		Line 25:
	[[Category: Sato, M.]]		[[Category: Sato, M.]]
	[[Category: Shimizu, T.]]		[[Category: Shimizu, T.]]
-	[[Category: Alternative splicing]]
	[[Category: Clamp]]		[[Category: Clamp]]
	[[Category: Complex]]		[[Category: Complex]]
Line 54:		Line 44:
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
	[[Category: Pip-box]]		[[Category: Pip-box]]
-	[[Category: Polymorphism]]
	[[Category: Schiff base]]		[[Category: Schiff base]]
	[[Category: Systemic lupus erythematosus]]		[[Category: Systemic lupus erythematosus]]
Line 61:		Line 50:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Translesion synthesis]]		[[Category: Translesion synthesis]]
-	[[Category: Ubl conjugation]]
	[[Category: Xeroderma pigmentosum]]		[[Category: Xeroderma pigmentosum]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 10:56:39 2009''

OCA at 07:56, 22 April 2009

OCA — Wed, 22 Apr 2009 07:56:40 GMT

←Older revision		Revision as of 07:56, 22 April 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:2zvk.~~jpg~~\|left\|200px]]	+	[[Image:2zvk.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Crystal structure of PCNA in complex with DNA polymerase eta fragment===		===Crystal structure of PCNA in complex with DNA polymerase eta fragment===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19208623}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19208623 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19208623}}

	==About this Structure==		==About this Structure==
	2ZVK is a 6 chains structure of sequences 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=2ZVK OCA].		2ZVK is a 6 chains structure of sequences 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=2ZVK OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19208623</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 55:		Line 64:
	[[Category: Xeroderma pigmentosum]]		[[Category: Xeroderma pigmentosum]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 11 12~~:38:58 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 10:56:39 2009''