6f5b - Revision history

OCA at 07:32, 1 May 2024

OCA — Wed, 01 May 2024 07:32:15 GMT

←Older revision		Revision as of 07:32, 1 May 2024
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	<StructureSection load='6f5b' size='340' side='right'caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6f5b' size='340' side='right'caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f5b]] 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=6F5B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6F5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f5b]] 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=6F5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F5B FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PARP2, ADPRT2, ADPRTL2 ([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]] 2.8Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_ADP~~-~~ribosyltransferase NAD(+) ADP-ribosyltransferase]~~, ~~with EC number~~ [~~http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.~~4.2.30 2.4.2.30] </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=6f5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f5b OCA], [https://pdbe.org/6f5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f5b RCSB], [https://www.ebi.ac.uk/pdbsum/6f5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f5b ProSAT]</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=6f5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f5b OCA], [~~http~~://pdbe.org/6f5b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6f5b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6f5b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6f5b ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PARP2_HUMAN PARP2_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks.	+	[https://www.uniprot.org/uniprot/PARP2_HUMAN PARP2_HUMAN] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Human ARTD2 (or PARP2) is an ADP-ribosyltransferase, which is catalytically activated by binding to damaged DNA. ARTD2 subsequently ADP-ribosylates itself and other proteins, initiating a cascade of events leading to DNA repair. In contrast to ARTD1, the founding member of the enzyme family, ARTD2 does not have specialized zinc-fingers for detecting DNA damage. The domain organization of ARTD2 includes disordered N-terminus, WGR and catalytic domains. However, the N-terminus of ARTD2 is not strictly required for the DNA dependent activity. While it is known that ARTD2 requires the WGR domain for efficient DNA binding and subsequent catalytic activation, the mechanism of DNA damage detection and subsequent catalytic activation are not completely understood. Here, we report crystal structures of ARTD2 WGR domain bound to double-strand break mimicking DNA oligonucleotides. Notably, the crystal structures revealed DNA binding mode of ARTD2 involving DNA end to end interaction. Structures demonstrate how ARTD2 recognizes nicked DNA, how it interacts with the 5'-phosphate group, and how it can mediate joining of DNA ends in vitro. Extensive mutagenesis of the ARTD2-DNA interface combined with activity, binding, and stoichiometry measurements demonstrate that the WGR domain is the key for DNA break detection.	+

-	~~Structural basis for DNA break recognition by ARTD2/PARP2.,Obaji E, Haikarainen T, Lehtio L Nucleic Acids Res. 2018 Oct 13. pii: 5128921. doi: 10.1093/nar/gky927. PMID:30321391<ref>PMID:30321391</ref>~~	+	==See Also==
-		+	*[[Poly(ADP-ribose) polymerase 3D structures\|Poly(ADP-ribose) polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6f5b" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Haikarainen, T]]	+	[[Category: Haikarainen T]]
-	[[Category: Lehtio, L]]	+	[[Category: Lehtio L]]
-	[[Category: Obaji, E]]	+	[[Category: Obaji E]]
-	~~[[Category: Adp-ribosylation]]~~	+
-	~~[[Category: Artd2]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna end joining]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Phosphorylated dna~~]]	+

OCA at 07:11, 16 October 2019

OCA — Wed, 16 Oct 2019 07:11:45 GMT

←Older revision		Revision as of 07:11, 16 October 2019
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	==Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate==		==Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate==
-	<StructureSection load='6f5b' size='340' side='right' caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='6f5b' size='340' side='right'caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6f5b]] 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=6F5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F5B FirstGlance]. <br>		<table><tr><td colspan='2'>[[6f5b]] 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=6F5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F5B FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Haikarainen, T]]		[[Category: Haikarainen, T]]
	[[Category: Lehtio, L]]		[[Category: Lehtio, L]]

OCA at 06:56, 24 October 2018

OCA — Wed, 24 Oct 2018 06:56:06 GMT

←Older revision		Revision as of 06:56, 24 October 2018
Line 3:		Line 3:
	<StructureSection load='6f5b' size='340' side='right' caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6f5b' size='340' side='right' caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f5b]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f5b]] 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=6F5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F5B FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.30 2.4.2.30] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PARP2, ADPRT2, ADPRTL2 ([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/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.30 2.4.2.30] </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=6f5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f5b OCA], [http://pdbe.org/6f5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f5b RCSB], [http://www.ebi.ac.uk/pdbsum/6f5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f5b ProSAT]</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=6f5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f5b OCA], [http://pdbe.org/6f5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f5b RCSB], [http://www.ebi.ac.uk/pdbsum/6f5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f5b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PARP2_HUMAN PARP2_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks.		[[http://www.uniprot.org/uniprot/PARP2_HUMAN PARP2_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human ARTD2 (or PARP2) is an ADP-ribosyltransferase, which is catalytically activated by binding to damaged DNA. ARTD2 subsequently ADP-ribosylates itself and other proteins, initiating a cascade of events leading to DNA repair. In contrast to ARTD1, the founding member of the enzyme family, ARTD2 does not have specialized zinc-fingers for detecting DNA damage. The domain organization of ARTD2 includes disordered N-terminus, WGR and catalytic domains. However, the N-terminus of ARTD2 is not strictly required for the DNA dependent activity. While it is known that ARTD2 requires the WGR domain for efficient DNA binding and subsequent catalytic activation, the mechanism of DNA damage detection and subsequent catalytic activation are not completely understood. Here, we report crystal structures of ARTD2 WGR domain bound to double-strand break mimicking DNA oligonucleotides. Notably, the crystal structures revealed DNA binding mode of ARTD2 involving DNA end to end interaction. Structures demonstrate how ARTD2 recognizes nicked DNA, how it interacts with the 5'-phosphate group, and how it can mediate joining of DNA ends in vitro. Extensive mutagenesis of the ARTD2-DNA interface combined with activity, binding, and stoichiometry measurements demonstrate that the WGR domain is the key for DNA break detection.
		+
		+	Structural basis for DNA break recognition by ARTD2/PARP2.,Obaji E, Haikarainen T, Lehtio L Nucleic Acids Res. 2018 Oct 13. pii: 5128921. doi: 10.1093/nar/gky927. PMID:30321391<ref>PMID:30321391</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6f5b" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Haikarainen, T]]		[[Category: Haikarainen, T]]
	[[Category: Lehtio, L]]		[[Category: Lehtio, L]]

OCA at 08:11, 10 October 2018

OCA — Wed, 10 Oct 2018 08:11:36 GMT

←Older revision		Revision as of 08:11, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6f5b is ~~ON HOLD~~	+	==Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate==
-		+	<StructureSection load='6f5b' size='340' side='right' caption='[[6f5b]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6f5b]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F5B FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.30 2.4.2.30] </span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6f5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f5b OCA], [http://pdbe.org/6f5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f5b RCSB], [http://www.ebi.ac.uk/pdbsum/6f5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f5b ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PARP2_HUMAN PARP2_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Haikarainen, T]]
		+	[[Category: Lehtio, L]]
		+	[[Category: Obaji, E]]
		+	[[Category: Adp-ribosylation]]
		+	[[Category: Artd2]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna end joining]]
		+	[[Category: Dna repair]]
		+	[[Category: Phosphorylated dna]]

OCA: Protected "6f5b" [edit=sysop:move=sysop]

OCA — Wed, 06 Dec 2017 06:19:08 GMT

Protected "6f5b" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:19, 6 December 2017

OCA: New page: '''Unreleased structure''' The entry 6f5b is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 Dec 2017 06:19:07 GMT

New page: '''Unreleased structure''' The entry 6f5b is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6f5b is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]