6k3a - Revision history

OCA at 10:26, 22 November 2023

OCA — Wed, 22 Nov 2023 10:26:08 GMT

←Older revision		Revision as of 10:26, 22 November 2023
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	<StructureSection load='6k3a' size='340' side='right'caption='[[6k3a]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6k3a' size='340' side='right'caption='[[6k3a]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k3a]] 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=6K3A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k3a]] 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=6K3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K3A FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</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=6k3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k3a OCA], [~~http~~://pdbe.org/6k3a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k3a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k3a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k3a 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=6k3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k3a OCA], [https://pdbe.org/6k3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k3a RCSB], [https://www.ebi.ac.uk/pdbsum/6k3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k3a 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6k3a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k3a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proliferating cell nuclear antigen 3D structures\|Proliferating cell nuclear antigen 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arita, K]]	+	[[Category: Arita K]]
-	[[Category: Jimenji, T]]	+	[[Category: Jimenji T]]
-	[[Category: Kori, S]]	+	[[Category: Kori S]]
-	~~[[Category: Dna methylation]]~~	+
-	~~[[Category: Dnmt1]]~~	+
-	~~[[Category: Pcna]]~~	+
-	~~[[Category: Pip box]]~~	+
-	~~[[Category: Replication~~]]	+

OCA at 06:27, 10 July 2019

OCA — Wed, 10 Jul 2019 06:27:11 GMT

←Older revision		Revision as of 06:27, 10 July 2019
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	<StructureSection load='6k3a' size='340' side='right'caption='[[6k3a]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6k3a' size='340' side='right'caption='[[6k3a]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k3a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k3a]] 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=6K3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K3A FirstGlance]. <br>
-	</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=6k3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k3a OCA], [http://pdbe.org/6k3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k3a RCSB], [http://www.ebi.ac.uk/pdbsum/6k3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k3a ProSAT]</span></td></tr>	+	</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='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=6k3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k3a OCA], [http://pdbe.org/6k3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k3a RCSB], [http://www.ebi.ac.uk/pdbsum/6k3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k3a 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>		[[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNMT1 is a C5-DNA methyltransferase that plays a pivotal role in DNA methylation maintenance. During early and mid S-phase, DNMT1 accumulates at DNA replication sites by binding to proliferating cell nuclear antigen (PCNA), an essential factor for DNA replication, through a PIP box motif. However, the molecular mechanism by which the DNMT1 PIP box motif binds to PCNA remains unclear. Here, we report the crystal structure of PCNA bound to DNMT1 PIP box peptide. The structure reveals the detailed interaction between PCNA and DNMT1 PIP box; conserved glutamine and hydrophobic/aromatic residues in the PIP box are recognized by the Q- and hydrophobic pockets of PCNA, respectively. The structure also shows novel intramolecular interactions within the PIP box motif, which stabilize the helix conformation in the PIP box. Our data provide structural insight into the recruitment of DNMT1 to replication sites by PCNA.
		+
		+	Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction.,Jimenji T, Matsumura R, Kori S, Arita K Biochem Biophys Res Commun. 2019 Jun 21. pii: S0006-291X(19)31196-9. doi:, 10.1016/j.bbrc.2019.06.060. PMID:31235252<ref>PMID:31235252</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k3a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Arita, K]]		[[Category: Arita, K]]

OCA at 06:54, 26 June 2019

OCA — Wed, 26 Jun 2019 06:54:33 GMT

←Older revision		Revision as of 06:54, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k3a ~~is ON HOLD~~	+	==Crystal structure of human PCNA in complex with DNMT1 PIP box motif.==
-		+	<StructureSection load='6k3a' size='340' side='right'caption='[[6k3a]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k3a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K3A FirstGlance]. <br>
-	~~Description~~:	+	</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=6k3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k3a OCA], [http://pdbe.org/6k3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k3a RCSB], [http://www.ebi.ac.uk/pdbsum/6k3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k3a ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Arita, K]]
		+	[[Category: Jimenji, T]]
		+	[[Category: Kori, S]]
		+	[[Category: Dna methylation]]
		+	[[Category: Dnmt1]]
		+	[[Category: Pcna]]
		+	[[Category: Pip box]]
		+	[[Category: Replication]]

OCA: Protected "6k3a" [edit=sysop:move=sysop]

OCA — Wed, 22 May 2019 03:57:38 GMT

Protected "6k3a" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:57, 22 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k3a is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 May 2019 03:57:36 GMT

New page: '''Unreleased structure''' The entry 6k3a is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6k3a is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]