3ode - Revision history

OCA at 10:33, 21 February 2024

2024-02-21T10:33:55Z

← Older revision		Revision as of 10:33, 21 February 2024
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	<StructureSection load='3ode' size='340' side='right'caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='3ode' size='340' side='right'caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ODE FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ODE FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.95Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3od8\|3od8]]~~, [[~~3oda~~\|~~3oda]], [[3odc\|3odc~~]]~~</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ADPRT, PARP1, PPOL ([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/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [https://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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [https://pdbe.org/3ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [https://www.ebi.ac.uk/pdbsum/3ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ode 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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [https://pdbe.org/3ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [https://www.ebi.ac.uk/pdbsum/3ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ode ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_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. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>		[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_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. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.

	Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY.,Langelier MF, Planck JL, Roy S, Pascal JM J Biol Chem. 2011 Mar 25;286(12):10690-701. Epub 2011 Jan 13. PMID:21233213<ref>PMID:21233213</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3ode" style="background-color:#fffaf0;"></div~~>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Langelier, M F]]		[[Category: Langelier M-F]]
	[[Category: Pascal~~, J M]]~~		[[Category: Pascal JM]]
	~~[[Category: Dna binding protein-dna complex]]~~
	~~[[Category: Parp zinc finger]]~~
	~~[[Category: Protein-dna complex~~]]

OCA at 10:40, 18 May 2022

2022-05-18T10:40:26Z

← Older revision		Revision as of 10:40, 18 May 2022
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	==Human PARP-1 zinc finger 2 (Zn2) bound to DNA==		==Human PARP-1 zinc finger 2 (Zn2) bound to DNA==
	<StructureSection load='3ode' size='340' side='right' caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='3ode' size='340' side='right'caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ODE FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ODE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3od8\|3od8]], [[3oda\|3oda]], [[3odc\|3odc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3od8\|3od8]], [[3oda\|3oda]], [[3odc\|3odc]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRT, PARP1, PPOL ([~~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">ADPRT, PARP1, PPOL ([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/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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [https://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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [~~http~~://pdbe.org/3ode PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ode PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ode 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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [https://pdbe.org/3ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [https://www.ebi.ac.uk/pdbsum/3ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ode ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_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. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>		[[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_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. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</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 3ode" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ode" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Poly(ADP-ribose) polymerase 3D structures\|Poly(ADP-ribose) polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Langelier, M F]]		[[Category: Langelier, M F]]
	[[Category: Pascal, J M]]		[[Category: Pascal, J M]]

OCA at 08:43, 8 November 2017

2017-11-08T08:43:38Z

← Older revision		Revision as of 08:43, 8 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3ode" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ode" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Poly (ADP-ribose) polymerase\|Poly (ADP-ribose) polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:53, 4 August 2016

2016-08-04T19:53:58Z

← Older revision		Revision as of 19:53, 4 August 2016
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	==Human PARP-1 zinc finger 2 (Zn2) bound to DNA==		==Human PARP-1 zinc finger 2 (Zn2) bound to DNA==
	<StructureSection load='3ode' size='340' side='right' caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='3ode' size='340' side='right' caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ODE FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ODE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3od8\|3od8]], [[3oda\|3oda]], [[3odc\|3odc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3od8\|3od8]], [[3oda\|3oda]], [[3odc\|3odc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRT, PARP1, PPOL ([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">ADPRT, PARP1, PPOL ([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='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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [http://www.ebi.ac.uk/pdbsum/3ode 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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [http://pdbe.org/3ode PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [http://www.ebi.ac.uk/pdbsum/3ode PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ode ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 3ode" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Langelier, M F]]		[[Category: Langelier, M F]]
	[[Category: Pascal, J M]]		[[Category: Pascal, J M]]

OCA at 12:35, 25 December 2014

2014-12-25T12:35:53Z

← Older revision		Revision as of 12:35, 25 December 2014
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	<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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [http://www.ebi.ac.uk/pdbsum/3ode 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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [http://www.ebi.ac.uk/pdbsum/3ode PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_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. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:05, 9 December 2014

2014-12-09T12:05:14Z

← Older revision		Revision as of 12:05, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~3ode~~.~~png~~\|~~left~~\|~~200px~~]]		==Human PARP-1 zinc finger 2 (Zn2) bound to DNA==
			<StructureSection load='3ode' size='340' side='right' caption='[[3ode]], [[Resolution\|resolution]] 2.95Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3ode]] 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=3ODE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ODE FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3od8\|3od8]], [[3oda\|3oda]], [[3odc\|3odc]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADPRT, PARP1, PPOL ([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/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=3ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ode OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ode RCSB], [http://www.ebi.ac.uk/pdbsum/3ode PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.

	~~{{STRUCTURE_3ode\| PDB=3ode \| SCENE= }}~~		Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY.,Langelier MF, Planck JL, Roy S, Pascal JM J Biol Chem. 2011 Mar 25;286(12):10690-701. Epub 2011 Jan 13. PMID:21233213<ref>PMID:21233213</ref>

	~~===Human PARP-1 zinc finger 2 (Zn2) bound to DNA===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_21233213}}~~

	~~==About this Structure==~~
	~~[[3ode]] 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=3ODE OCA].~~

	==See Also==		==See Also==
	*[[Poly (ADP-ribose) polymerase\|Poly (ADP-ribose) polymerase]]		*[[Poly (ADP-ribose) polymerase\|Poly (ADP-ribose) polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:021233213<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Langelier, M F.]]		[[Category: Langelier, M F]]
	[[Category: Pascal, J M.]]		[[Category: Pascal, J M]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]
	[[Category: Parp zinc finger]]		[[Category: Parp zinc finger]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 16:44, 20 October 2012

2012-10-20T16:44:33Z

← Older revision		Revision as of 16:44, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3ode]] is a 6 chain structure ~~of [[Poly (ADP-ribose) 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=3ODE OCA].		[[3ode]] 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=3ODE OCA].

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

OCA at 22:41, 26 July 2012

2012-07-26T22:41:31Z

← Older revision		Revision as of 22:41, 26 July 2012
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	[[Image:3ode.png\|left\|200px]]		[[Image:3ode.png\|left\|200px]]

	~~<!--~~
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	~~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.~~
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	{{STRUCTURE_3ode\| PDB=3ode \| SCENE= }}		{{STRUCTURE_3ode\| PDB=3ode \| SCENE= }}

	===Human PARP-1 zinc finger 2 (Zn2) bound to DNA===		===Human PARP-1 zinc finger 2 (Zn2) bound to DNA===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_21233213}}, adds the Publication Abstract to the page~~
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	==See Also==		==See Also==
	*[[Poly (ADP-ribose) polymerase]]		*[[Poly (ADP-ribose) polymerase\|Poly (ADP-ribose) polymerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~21233213~~</ref><references group="xtra"/>		<ref group="xtra">PMID:021233213</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Langelier, M F.]]		[[Category: Langelier, M F.]]
	[[Category: Pascal, J M.]]		[[Category: Pascal, J M.]]
			[[Category: Dna binding protein-dna complex]]
			[[Category: Parp zinc finger]]
			[[Category: Protein-dna complex]]

OCA at 04:33, 13 April 2011

2011-04-13T04:33:31Z

← Older revision		Revision as of 04:33, 13 April 2011
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	[[Image:3ode.~~jpg~~\|left\|200px]]		[[Image:3ode.png\|left\|200px]]

	<!--		<!--
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	===Human PARP-1 zinc finger 2 (Zn2) bound to DNA===		===Human PARP-1 zinc finger 2 (Zn2) bound to DNA===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_21233213}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 21233213 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_21233213}}

	==About this Structure==		==About this Structure==
	[[3ode]] 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=3ODE OCA].		[[3ode]] is a 6 chain structure of [[Poly (ADP-ribose) 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=3ODE OCA].

			==See Also==
			*[[Poly (ADP-ribose) polymerase]]

			==Reference==
			<ref group="xtra">PMID:21233213</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Langelier, M F.]]		[[Category: Langelier, M F.]]
	[[Category: Pascal, J M.]]		[[Category: Pascal, J M.]]

OCA at 05:16, 12 January 2011

2011-01-12T05:16:48Z

← Older revision		Revision as of 05:16, 12 January 2011
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	~~'''Unreleased structure'''~~		[[Image:3ode.jpg\|left\|200px]]

	The ~~entry~~ 3ode ~~is ON HOLD~~ ~~until Paper Publication~~		<!--
			The line below this paragraph, containing "STRUCTURE_3ode", creates the "Structure Box" on the page.
			You may change the PDB parameter (which sets the PDB file loaded into the applet)
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			or leave the SCENE parameter empty for the default display.
			-->
			{{STRUCTURE_3ode\| PDB=3ode \| SCENE= }}

	~~Authors: Pascal, J.M., Langelier, M.~~-F.		===Human PARP-1 zinc finger 2 (Zn2) bound to DNA===

	~~Description~~: ~~Human PARP~~-~~1 zinc finger 2 (Zn2) bound to DNA~~
			==About this Structure==
			[[3ode]] 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=3ODE OCA].
			[[Category: Homo sapiens]]
			[[Category: Langelier, M F.]]
			[[Category: Pascal, J M.]]