4f1i - Revision history

OCA at 04:28, 7 October 2022

OCA — Fri, 07 Oct 2022 04:28:29 GMT

←Older revision		Revision as of 04:28, 7 October 2022
Line 1:		Line 1:

	==Crystal structure of SeMet TDP2 from Caenorhabditis elegans==		==Crystal structure of SeMet TDP2 from Caenorhabditis elegans==
-	<StructureSection load='4f1i' size='340' side='right' caption='[[4f1i]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4f1i' size='340' side='right'caption='[[4f1i]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4f1i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caeel Caeel~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4F1I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4f1i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F1I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [https://pdbe.org/4f1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [https://www.ebi.ac.uk/pdbsum/4f1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f1i ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fpv\|4fpv]], [[4f1h\|4f1h]], [[4fva\|4fva]], [[4gew\|4gew]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Y63D3A.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])~~</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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [~~http~~://pdbe.org/4f1i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4f1i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4f1i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TYDP2_CAEEL TYDP2_CAEEL]] 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 (By similarity).	+	[https://www.uniprot.org/uniprot/TYDP2_CAEEL TYDP2_CAEEL] 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 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4f1i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4f1i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caeel~~]]	+	[[Category: Caenorhabditis elegans]]
-	[[Category: ~~Aihara, H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kurahashi, K~~]]	+	[[Category: Aihara H]]
-	[[Category: ~~Shi,~~ K]]	+	[[Category: Kurahashi K]]
-	[[Category: ~~5'-tyrosyl dna phosphodiesterase]]~~	+	[[Category: Shi K]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:13, 15 November 2017

OCA — Wed, 15 Nov 2017 08:13:00 GMT

←Older revision		Revision as of 08:13, 15 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 4f1i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4f1i" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:43, 5 August 2016

OCA — Fri, 05 Aug 2016 01:43:25 GMT

←Older revision		Revision as of 01:43, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of SeMet TDP2 from Caenorhabditis elegans==		==Crystal structure of SeMet TDP2 from Caenorhabditis elegans==
	<StructureSection load='4f1i' size='340' side='right' caption='[[4f1i]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4f1i' size='340' side='right' caption='[[4f1i]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4f1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Caenorhabditis_elegans Caenorhabditis elegans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F1I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4f1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F1I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fpv\|4fpv]], [[4f1h\|4f1h]], [[4fva\|4fva]], [[4gew\|4gew]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fpv\|4fpv]], [[4f1h\|4f1h]], [[4fva\|4fva]], [[4gew\|4gew]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Y63D3A.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 ~~Caenorhabditis elegans~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Y63D3A.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [http://www.ebi.ac.uk/pdbsum/4f1i 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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [http://pdbe.org/4f1i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [http://www.ebi.ac.uk/pdbsum/4f1i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f1i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4f1i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caenorhabditis elegans~~]]	+	[[Category: Caeel]]
	[[Category: Aihara, H]]		[[Category: Aihara, H]]
	[[Category: Kurahashi, K]]		[[Category: Kurahashi, K]]

OCA at 21:42, 24 December 2014

OCA — Wed, 24 Dec 2014 21:42:09 GMT

←Older revision		Revision as of 21:42, 24 December 2014
Line 9:		Line 9:
	<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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [http://www.ebi.ac.uk/pdbsum/4f1i 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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [http://www.ebi.ac.uk/pdbsum/4f1i PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYDP2_CAEEL TYDP2_CAEEL]] 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 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:55, 9 December 2014

OCA — Tue, 09 Dec 2014 16:55:26 GMT

←Older revision		Revision as of 16:55, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4f1i.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of SeMet TDP2 from Caenorhabditis elegans==
		+	<StructureSection load='4f1i' size='340' side='right' caption='[[4f1i]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4f1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F1I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fpv\|4fpv]], [[4f1h\|4f1h]], [[4fva\|4fva]], [[4gew\|4gew]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Y63D3A.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 Caenorhabditis elegans])</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=4f1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f1i RCSB], [http://www.ebi.ac.uk/pdbsum/4f1i PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DNA-repair enzyme Tdp2 resolves 5'-phosphotyrosyl DNA adducts and mediates resistance to anticancer drugs that target covalent topoisomerase-DNA complexes. Tdp2 also participates in key signaling pathways during development and tumorigenesis and cleaves a protein-RNA linkage during picornavirus replication. The crystal structure of zebrafish Tdp2 bound to DNA reveals a deep, narrow basic groove that selectively accommodates the 5' end of single-stranded DNA in a stretched conformation. The crystal structure of the full-length Caenorhabditis elegans Tdp2 shows that this groove can also accommodate an acidic peptide stretch in vitro, with glutamate and aspartate side chains occupying the DNA backbone phosphate-binding sites. This extensive molecular mimicry suggests a potential mechanism for autoregulation and interaction of Tdp2 with phosphorylated proteins in signaling. Our study provides a framework to interrogate functions of Tdp2 and develop inhibitors for chemotherapeutic and antiviral applications.

-	~~{{STRUCTURE_4f1i\| PDB=4f1i \| SCENE= }}~~	+	Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.,Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H Nat Struct Mol Biol. 2012 Dec;19(12):1372-7. doi: 10.1038/nsmb.2423. Epub 2012, Oct 28. PMID:23104058<ref>PMID:23104058</ref>

-	~~===Crystal structure~~ of ~~SeMet TDP2 from Caenorhabditis elegans===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_23104058}}~~	+	==See Also==
-		+	*[[Phosphodiesterase\|Phosphodiesterase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4f1i~~]] ~~is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA].~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Caenorhabditis elegans]]		[[Category: Caenorhabditis elegans]]
-	[[Category: Aihara, H.]]	+	[[Category: Aihara, H]]
-	[[Category: Kurahashi, K.]]	+	[[Category: Kurahashi, K]]
-	[[Category: Shi, K.]]	+	[[Category: Shi, K]]
	[[Category: 5'-tyrosyl dna phosphodiesterase]]		[[Category: 5'-tyrosyl dna phosphodiesterase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:12, 2 January 2013

OCA — Wed, 02 Jan 2013 08:12:37 GMT

←Older revision		Revision as of 08:12, 2 January 2013
Line 1:		Line 1:
-	[[Image:4f1i.~~jpg~~\|left\|200px]]	+	[[Image:4f1i.png\|left\|200px]]

	{{STRUCTURE_4f1i\| PDB=4f1i \| SCENE= }}		{{STRUCTURE_4f1i\| PDB=4f1i \| SCENE= }}
Line 5:		Line 5:
	===Crystal structure of SeMet TDP2 from Caenorhabditis elegans===		===Crystal structure of SeMet TDP2 from Caenorhabditis elegans===

		+	{{ABSTRACT_PUBMED_23104058}}

	==About this Structure==		==About this Structure==

OCA at 09:22, 31 October 2012

OCA — Wed, 31 Oct 2012 09:22:16 GMT

←Older revision		Revision as of 09:22, 31 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4f1i.jpg\|left\|200px]]

-	~~The entry~~ 4f1i ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4f1i\| PDB=4f1i \| SCENE= }}

-	~~Authors: Shi, K., Kurahashi, K., Aihara, H.~~	+	===Crystal structure of SeMet TDP2 from Caenorhabditis elegans===

-	~~Description: Crystal~~ structure ~~of SeMet TDP2~~ from Caenorhabditis elegans	+
		+	==About this Structure==
		+	[[4f1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F1I OCA].
		+	[[Category: Caenorhabditis elegans]]
		+	[[Category: Aihara, H.]]
		+	[[Category: Kurahashi, K.]]
		+	[[Category: Shi, K.]]
		+	[[Category: 5'-tyrosyl dna phosphodiesterase]]
		+	[[Category: Hydrolase]]

OCA at 07:14, 4 July 2012

OCA — Wed, 04 Jul 2012 07:14:13 GMT

←Older revision		Revision as of 07:14, 4 July 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4f1i is ON HOLD	+	The entry 4f1i is ON HOLD until Paper Publication

	Authors: Shi, K., Kurahashi, K., Aihara, H.		Authors: Shi, K., Kurahashi, K., Aihara, H.

	Description: Crystal structure of SeMet TDP2 from Caenorhabditis elegans		Description: Crystal structure of SeMet TDP2 from Caenorhabditis elegans

OCA: Protected "4f1i" [edit=sysop:move=sysop]

OCA — Wed, 16 May 2012 08:53:26 GMT

Protected "4f1i" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:53, 16 May 2012

OCA: New page: '''Unreleased structure''' The entry 4f1i is ON HOLD Authors: Shi, K., Kurahashi, K., Aihara, H. Description: Crystal structure of SeMet TDP2 from Caenorhabditis elegans

OCA — Wed, 16 May 2012 08:53:25 GMT

New page: '''Unreleased structure''' The entry 4f1i is ON HOLD Authors: Shi, K., Kurahashi, K., Aihara, H. Description: Crystal structure of SeMet TDP2 from Caenorhabditis elegans

New page

'''Unreleased structure'''

The entry 4f1i is ON HOLD

Authors: Shi, K., Kurahashi, K., Aihara, H.

Description: Crystal structure of SeMet TDP2 from Caenorhabditis elegans