5zad - Revision history

OCA at 08:50, 22 November 2023

OCA — Wed, 22 Nov 2023 08:50:44 GMT

←Older revision		Revision as of 08:50, 22 November 2023
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	<StructureSection load='5zad' size='340' side='right'caption='[[5zad]], [[Resolution\|resolution]] 2.54Å' scene=''>		<StructureSection load='5zad' size='340' side='right'caption='[[5zad]], [[Resolution\|resolution]] 2.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zad]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZAD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zad]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZAD FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3qx3\|3qx3]]</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]] 2.54Å</td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP~~-~~hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)]~~, ~~with EC number~~ [~~http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5zad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zad OCA], [https://pdbe.org/5zad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zad RCSB], [https://www.ebi.ac.uk/pdbsum/5zad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zad 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=5zad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zad OCA], [~~http~~://pdbe.org/5zad PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zad RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zad PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zad ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>	+	[https://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sun, L Y~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Tang, Y J~~]]	+	[[Category: Sun LY]]
-	[[Category: ~~Zhu, L W~~]]	+	[[Category: Tang YJ]]
-	[[Category: ~~Dna binding and cleavage]]~~	+	[[Category: Zhu LW]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Isomerase-dna complex~~]]	+

OCA at 07:40, 20 March 2019

OCA — Wed, 20 Mar 2019 07:40:22 GMT

←Older revision		Revision as of 07:40, 20 March 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5zad is ~~ON HOLD~~	+	==Human topoisomerase II beta in complex with DNA==
		+	<StructureSection load='5zad' size='340' side='right'caption='[[5zad]], [[Resolution\|resolution]] 2.54Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zad]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZAD FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qx3\|3qx3]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5zad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zad OCA], [http://pdbe.org/5zad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zad RCSB], [http://www.ebi.ac.uk/pdbsum/5zad PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zad ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Topoisomerases II (Top2s) are a group of essential enzymes involved in replication, transcription, chromosome condensation, and segregation via altering DNA topology. The mechanism of the Top2s poisons such as etoposide (VP-16) was reported as stabilizing the Top2-DNA complex and engendering permanent DNA breakage. As the structurally similar compound of VP-16, a novel 4beta-sulfur-substituted 4'-demethylepipodophyllotoxin (DMEP) derivative (compound C-Bi) with superior antitumor activity was developed in our previous study. To understand the structural basis of the compound action, the crystal structure (2.54 A) of human Top2 beta-isoform (hTop2beta) cleavage complexes stabilized by compound C-Bi was determined. However, compound C-Bi was not visible in the crystal structure. Through the comparison of the structures of hTop2beta-DNA-etoposide ternary complex and hTop2beta-DNA binary complex, it could be observed that the distance between drug-binding sites Arg503 of the two monomers was 26.62 A in hTop2beta-DNA-etoposide ternary complex and 34.54 A in hTop2beta-DNA binary complex, respectively. Significant twist were observed in the DNA chains of binary complex. It suggested that compound C-Bi played antitumor roles through increasing spacing of hTop2beta monomers. The changes in hTop2beta structure further caused double changes in the torsional direction and migration distance of the DNA chains, resulting in impeding religation of DNA.

-	~~Authors: Sun, L.Y~~., Zhu, L.W.~~, Tang, Y~~.J.	+	Increasing the distance between two monomers of topoisomerase IIbeta under the action of antitumor agent 4beta-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin.,Sun LY, Zhu LW, Tang YJ Sci Rep. 2018 Oct 8;8(1):14949. doi: 10.1038/s41598-018-33366-2. PMID:30297860<ref>PMID:30297860</ref>

-	~~Description~~: ~~Human topoisomerase II beta in complex with DNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Sun, L.Y]]	+	<div class="pdbe-citations 5zad" style="background-color:#fffaf0;"></div>
-	[[Category: Zhu, L.W]]	+	== References ==
-	[[Category: ~~Tang, Y.J~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sun, L Y]]
		+	[[Category: Tang, Y J]]
		+	[[Category: Zhu, L W]]
		+	[[Category: Dna binding and cleavage]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Isomerase-dna complex]]

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

OCA — Thu, 15 Feb 2018 05:11:52 GMT

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

←Older revision

Revision as of 05:11, 15 February 2018

OCA: New page: '''Unreleased structure''' The entry 5zad is ON HOLD Authors: Sun, L.Y., Zhu, L.W., Tang, Y.J. Description: Human topoisomerase II beta in complex with DNA [[Category: Unreleased Struc...

OCA — Thu, 15 Feb 2018 05:11:50 GMT

New page: '''Unreleased structure''' The entry 5zad is ON HOLD Authors: Sun, L.Y., Zhu, L.W., Tang, Y.J. Description: Human topoisomerase II beta in complex with DNA [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5zad is ON HOLD

Authors: Sun, L.Y., Zhu, L.W., Tang, Y.J.

Description: Human topoisomerase II beta in complex with DNA
[[Category: Unreleased Structures]]
[[Category: Sun, L.Y]]
[[Category: Zhu, L.W]]
[[Category: Tang, Y.J]]