5j5q - Revision history

OCA at 10:49, 6 September 2023

OCA — Wed, 06 Sep 2023 10:49:39 GMT

←Older revision		Revision as of 10:49, 6 September 2023
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	==AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II==		==AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II==
-	<StructureSection load='5j5q' size='340' side='right' caption='[[5j5q]], [[Resolution\|resolution]] 2.83Å' scene=''>	+	<StructureSection load='5j5q' size='340' side='right'caption='[[5j5q]], [[Resolution\|resolution]] 2.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j5q]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ] and [~~http~~://en.wikipedia.org/wiki/~~"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j5q]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae] 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=5J5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J5Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~ADENYLATE+ESTER'>ANP</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]] 2.83Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>parE, SP_0852 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1313~~ "~~Diplococcus pneumoniae~~" ~~(Klein 1884) Weichselbaum 1886])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5q OCA], [https://pdbe.org/5j5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j5q RCSB], [https://www.ebi.ac.uk/pdbsum/5j5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5q 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=5j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5q OCA], [~~http~~://pdbe.org/5j5q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j5q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j5q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN]] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>	+	[https://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Topoisomerase\|Topoisomerase]]	+	*[[Topoisomerase 3D structures\|Topoisomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Fisher, L M]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Laponogov, I]]~~	+
-	~~[[Category: Pan, X S]]~~	+
-	~~[[Category: Sanderson, M R]]~~	+
-	~~[[Category: Skamrova, G]]~~	+
-	~~[[Category: Umrekar, T]]~~	+
-	~~[[Category: Atpase domain]]~~	+
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Isomerase-dna complex~~]]	+
	[[Category: Streptococcus pneumoniae]]		[[Category: Streptococcus pneumoniae]]
-	[[Category: T-~~segment~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Topoisomerase iv~~]]	+	[[Category: Fisher LM]]
		+	[[Category: Laponogov I]]
		+	[[Category: Pan X-S]]
		+	[[Category: Sanderson MR]]
		+	[[Category: Skamrova G]]
		+	[[Category: Umrekar T]]

OCA at 08:46, 18 July 2018

OCA — Wed, 18 Jul 2018 08:46:36 GMT

←Older revision		Revision as of 08:46, 18 July 2018
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN]] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>		[[http://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN]] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Type II topoisomerases alter DNA topology to control DNA supercoiling and chromosome segregation and are targets of clinically important anti-infective and anticancer therapeutics. They act as ATP-operated clamps to trap a DNA helix and transport it through a transient break in a second DNA. Here, we present the first X-ray crystal structure solved at 2.83 A of a closed clamp complete with trapped T-segment DNA obtained by co-crystallizing the ATPase domain of S. pneumoniae topoisomerase IV with a nonhydrolyzable ATP analogue and 14-mer duplex DNA. The ATPase dimer forms a 22 A protein hole occupied by the kinked DNA bound asymmetrically through positively charged residues lining the hole, and whose mutagenesis impacts the DNA decatenation, DNA relaxation and DNA-dependent ATPase activities of topo IV. These results and a side-bound DNA-ParE structure help explain how the T-segment DNA is captured and transported by a type II topoisomerase, and reveal a new enzyme-DNA interface for drug discovery.
		+
		+	Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase.,Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR Nat Commun. 2018 Jul 3;9(1):2579. doi: 10.1038/s41467-018-05005-x. PMID:29968711<ref>PMID:29968711</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j5q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Topoisomerase\|Topoisomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:37, 16 November 2017

OCA — Thu, 16 Nov 2017 04:37:37 GMT

←Older revision		Revision as of 04:37, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j5q is ~~ON HOLD~~ ~~until Paper Publication~~	+	==AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II==
-		+	<StructureSection load='5j5q' size='340' side='right' caption='[[5j5q]], [[Resolution\|resolution]] 2.83Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j5q]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J5Q FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">parE, SP_0852 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</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=5j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j5q OCA], [http://pdbe.org/5j5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j5q RCSB], [http://www.ebi.ac.uk/pdbsum/5j5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j5q ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PARE_STRPN PARE_STRPN]] Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.<ref>PMID:17375187</ref> <ref>PMID:20596531</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fisher, L M]]
		+	[[Category: Laponogov, I]]
		+	[[Category: Pan, X S]]
		+	[[Category: Sanderson, M R]]
		+	[[Category: Skamrova, G]]
		+	[[Category: Umrekar, T]]
		+	[[Category: Atpase domain]]
		+	[[Category: Dna binding]]
		+	[[Category: Isomerase-dna complex]]
		+	[[Category: Streptococcus pneumoniae]]
		+	[[Category: T-segment]]
		+	[[Category: Topoisomerase iv]]

OCA at 15:05, 15 May 2016

OCA — Sun, 15 May 2016 15:05:00 GMT

←Older revision		Revision as of 15:05, 15 May 2016
Line 3:		Line 3:
	The entry 5j5q is ON HOLD until Paper Publication		The entry 5j5q is ON HOLD until Paper Publication

-	Authors: ~~Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Fisher, L.M]]
-	[[Category: Laponogov, I]]
-	[[Category: Umrekar, T]]
-	[[Category: Skamrova, G]]
-	[[Category: Pan, X.-S]]
-	[[Category: Sanderson, M.R]]

OCA: Protected "5j5q" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:30:15 GMT

Protected "5j5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:30, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j5q is ON HOLD until Paper Publication Authors: Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R. Description: ...

OCA — Wed, 11 May 2016 01:30:14 GMT

New page: '''Unreleased structure''' The entry 5j5q is ON HOLD until Paper Publication Authors: Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R. Description: ...

New page

'''Unreleased structure'''

The entry 5j5q is ON HOLD until Paper Publication

Authors: Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.

Description:
[[Category: Unreleased Structures]]
[[Category: Fisher, L.M]]
[[Category: Laponogov, I]]
[[Category: Umrekar, T]]
[[Category: Skamrova, G]]
[[Category: Pan, X.-S]]
[[Category: Sanderson, M.R]]