5j3z - Revision history

OCA at 10:45, 6 September 2023

OCA — Wed, 06 Sep 2023 10:45:56 GMT

←Older revision		Revision as of 10:45, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5j3z' size='340' side='right'caption='[[5j3z]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5j3z' size='340' side='right'caption='[[5j3z]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tdp2, Ttrap ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [~~http~~://pdbe.org/5j3z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j3z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3z 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=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [https://pdbe.org/5j3z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [https://www.ebi.ac.uk/pdbsum/5j3z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TYDP2_MOUSE TYDP2_MOUSE]] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 5'-phosphodiester bond, giving rise to DNA with a free 5' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase 2 (TOP2) active site tyrosine residue. Hydrolyzes 5'-phosphoglycolates on protruding 5' ends on DNA double-strand breaks (DSBs) due to DNA damage by radiation and free radicals. The 5'-tyrosyl DNA phosphodiesterase activity can enable the repair of TOP2-induced DSBs without the need for nuclease activity, creating a 'clean' DSB with 5'-phosphate termini that are ready for ligation. Has preference for single-stranded DNA or duplex DNA with a 4 base pair overhang as substrate. Has also 3'-tyrosyl DNA phosphodiesterase activity, but less efficiently and much slower than TDP1. Constitutes the major if not only 5'-tyrosyl-DNA phosphodiesterase in cells. Also acts as an adapter by participating in the specific activation of MAP3K7/TAK1 in response to TGF-beta: associates with components of the TGF-beta receptor-TRAF6-TAK1 signaling module and promotes their ubiquitination dependent complex formation. Involved in non-canonical TGF-beta induced signaling routes. May also act as a negative regulator of ETS1 and may inhibit NF-kappa-B activation. Acts as a regulator of ribosome biogenesis following stress.<ref>PMID:22740648</ref>	+	[https://www.uniprot.org/uniprot/TYDP2_MOUSE TYDP2_MOUSE] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 5'-phosphodiester bond, giving rise to DNA with a free 5' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase 2 (TOP2) active site tyrosine residue. Hydrolyzes 5'-phosphoglycolates on protruding 5' ends on DNA double-strand breaks (DSBs) due to DNA damage by radiation and free radicals. The 5'-tyrosyl DNA phosphodiesterase activity can enable the repair of TOP2-induced DSBs without the need for nuclease activity, creating a 'clean' DSB with 5'-phosphate termini that are ready for ligation. Has preference for single-stranded DNA or duplex DNA with a 4 base pair overhang as substrate. Has also 3'-tyrosyl DNA phosphodiesterase activity, but less efficiently and much slower than TDP1. Constitutes the major if not only 5'-tyrosyl-DNA phosphodiesterase in cells. Also acts as an adapter by participating in the specific activation of MAP3K7/TAK1 in response to TGF-beta: associates with components of the TGF-beta receptor-TRAF6-TAK1 signaling module and promotes their ubiquitination dependent complex formation. Involved in non-canonical TGF-beta induced signaling routes. May also act as a negative regulator of ETS1 and may inhibit NF-kappa-B activation. Acts as a regulator of ribosome biogenesis following stress.<ref>PMID:22740648</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Caldecott~~, K W~~]]	+	[[Category: Caldecott KW]]
-	[[Category: Hornyak, P]]	+	[[Category: Hornyak P]]
-	[[Category: Oliver~~, A W~~]]	+	[[Category: Oliver AW]]
-	[[Category: Pearl~~, L H]]~~	+	[[Category: Pearl LH]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tyrosyl dna phosphodiesterase 2 catalytic domain~~]]	+

OCA at 07:28, 10 June 2020

OCA — Wed, 10 Jun 2020 07:28:19 GMT

←Older revision		Revision as of 07:28, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor==		==Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor==
-	<StructureSection load='5j3z' size='340' side='right' caption='[[5j3z]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5j3z' size='340' side='right'caption='[[5j3z]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [http://pdbe.org/5j3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [http://www.ebi.ac.uk/pdbsum/5j3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3z ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tdp2, Ttrap ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [http://pdbe.org/5j3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [http://www.ebi.ac.uk/pdbsum/5j3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5j3z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5j3z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Caldecott, K W]]		[[Category: Caldecott, K W]]
	[[Category: Hornyak, P]]		[[Category: Hornyak, P]]

OCA at 17:30, 12 July 2016

OCA — Tue, 12 Jul 2016 17:30:22 GMT

←Older revision		Revision as of 17:30, 12 July 2016
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [http://pdbe.org/5j3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [http://www.ebi.ac.uk/pdbsum/5j3z 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=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [http://pdbe.org/5j3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [http://www.ebi.ac.uk/pdbsum/5j3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA: Protected "5j3z" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 03:26:45 GMT

Protected "5j3z" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:26, 11 May 2016

OCA: New page: ==Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor== == Structural highlights ==
<table><tr><td colspan='2'>[[5j3z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3Z FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FQ:2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE'>6FQ</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5j3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3z OCA], [http://pdbe.org/5j3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3z RCSB], [http://www.ebi.ac.uk/pdbsum/5j3z PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/TYDP2_MOUSE TYDP2_MOUSE]] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 5'-phosphodiester bond, giving rise to DNA with a free 5' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase 2 (TOP2) active site tyrosine residue. Hydrolyzes 5'-phosphoglycolates on protruding 5' ends on DNA double-strand breaks (DSBs) due to DNA damage by radiation and free radicals. The 5'-tyrosyl DNA phosphodiesterase activity can enable the repair of TOP2-induced DSBs without the need for nuclease activity, creating a 'clean' DSB with 5'-phosphate termini that are ready for ligation. Has preference for single-stranded DNA or duplex DNA with a 4 base pair overhang as substrate. Has also 3'-tyrosyl DNA phosphodiesterase activity, but less efficiently and much slower than TDP1. Constitutes the major if not only 5'-tyrosyl-DNA phosphodiesterase in cells. Also acts as an adapter by participating in the specific activation of MAP3K7/TAK1 in response to TGF-beta: associates with components of the TGF-beta receptor-TRAF6-TAK1 signaling module and promotes their ubiquitination dependent complex formation. Involved in non-canonical TGF-beta induced signaling routes. May also act as a negative regulator of ETS1 and may inhibit NF-kappa-B activation. Acts as a regulator of ribosome biogenesis following stress.<ref>PMID:22740648</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
TDP2 is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II. TDP2 facilitates therapeutic resistance to topoisomerase poisons, which are widely used in the treatment of a range of cancer types. Consequently, TDP2 is an interesting target for the development of small molecule inhibitors that could restore sensitivity to topoisomerase-directed therapies. Previous studies identified a class of deazaflavin-based molecules that showed inhibitory activity against TDP2 at therapeutically useful concentrations, but their mode of action was uncertain. We have confirmed that the deazaflavin series inhibits TDP2 enzyme activity in a fluorescence-based assay, suitable for HTS-screening. We have gone on to determine crystal structures of these compounds bound to a 'humanised' form of murine TDP2. The structures reveal their novel mode of action as competitive ligands for the binding site of an incoming DNA substrate, and point the way to generating novel and potent inhibitors of TDP2.

Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.,Hornyak P, Askwith T, Walker S, Komulainen E, Paradowski M, Pennicott LE, Bartlett EJ, Brissett NC, Raoof A, Watson M, Jordan AM, Ogilvie DJ, Ward SE, Atack JR, Pearl LH, Caldecott KW, Oliver AW Biochem J. 2016 Apr 20. pii: BCJ20160180. PMID:27099339<ref>PMID:27099339</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5j3z" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Caldecott, K W]]
[[Category: Hornyak, P]]
[[Category: Oliver, A W]]
[[Category: Pearl, L H]]
[[Category: Hydrolase]]
[[Category: Tyrosyl dna phosphodiesterase 2 catalytic domain]]