2o19 - Revision history

OCA at 10:28, 30 August 2023

2023-08-30T10:28:35Z

←Older revision		Revision as of 10:28, 30 August 2023
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	<StructureSection load='2o19' size='340' side='right'caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2o19' size='340' side='right'caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O19 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O19 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.45Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>topB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2]~~ </~~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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [https://pdbe.org/2o19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [https://www.ebi.ac.uk/pdbsum/2o19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o19 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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [https://pdbe.org/2o19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [https://www.ebi.ac.uk/pdbsum/2o19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o19 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TOP3_ECOLI TOP3_ECOLI]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. TOP3 is a potent decatenase.<ref>PMID:2553698</ref> <ref>PMID:6326814</ref>	+	[https://www.uniprot.org/uniprot/TOP3_ECOLI TOP3_ECOLI] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. TOP3 is a potent decatenase.<ref>PMID:2553698</ref> <ref>PMID:6326814</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: DNA topoisomerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Changela, A]]	+	[[Category: Changela A]]
-	[[Category: DiGate, R]]	+	[[Category: DiGate R]]
-	[[Category: Mondragon, A]]	+	[[Category: Mondragon A]]
-	~~[[Category: Complex with ssdna]]~~	+
-	~~[[Category: Isomerase-dna complex]]~~	+
-	~~[[Category: Topoisomerase]]~~	+
-	~~[[Category: Type ia~~]]	+

OCA at 15:57, 8 June 2021

2021-06-08T15:57:21Z

←Older revision		Revision as of 15:57, 8 June 2021
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	==Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5==		==Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5==
-	<StructureSection load='2o19' size='340' side='right' caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='2o19' size='340' side='right'caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2O19 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O19 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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 DNA topoisomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [~~http~~://pdbe.org/2o19 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2o19 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2o19 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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [https://pdbe.org/2o19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [https://www.ebi.ac.uk/pdbsum/2o19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o19 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TOP3_ECOLI TOP3_ECOLI]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. TOP3 is a potent decatenase.<ref>PMID:2553698</ref> <ref>PMID:6326814</ref>	+	[[https://www.uniprot.org/uniprot/TOP3_ECOLI TOP3_ECOLI]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. TOP3 is a potent decatenase.<ref>PMID:2553698</ref> <ref>PMID:6326814</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o1/2o19_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o1/2o19_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2o19" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2o19" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Topoisomerase 3D structures\|Topoisomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: DNA topoisomerase]]		[[Category: DNA topoisomerase]]
		+	[[Category: Large Structures]]
	[[Category: Changela, A]]		[[Category: Changela, A]]
	[[Category: DiGate, R]]		[[Category: DiGate, R]]

OCA at 08:49, 18 October 2017

2017-10-18T08:49:13Z

←Older revision		Revision as of 08:49, 18 October 2017
Line 1:		Line 1:
		+
	==Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5==		==Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5==
	<StructureSection load='2o19' size='340' side='right' caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2o19' size='340' side='right' caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://pdbe.org/2o19 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://pdbe.org/2o19 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o19 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 2o19" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2o19" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Topoisomerase\|Topoisomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:21, 7 February 2016

2016-02-07T05:21:18Z

←Older revision		Revision as of 05:21, 7 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2o19 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:14, 9 September 2015

2015-09-09T22:14:34Z

←Older revision		Revision as of 22:14, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2o19' size='340' side='right' caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2o19' size='340' side='right' caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O19 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O19 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://pdbe.org/2o19 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2o19" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: DNA topoisomerase]]		[[Category: DNA topoisomerase]]
-	[[Category: Escherichia coli]]
	[[Category: Changela, A]]		[[Category: Changela, A]]
	[[Category: DiGate, R]]		[[Category: DiGate, R]]

OCA at 08:09, 24 December 2014

2014-12-24T08:09:17Z

←Older revision		Revision as of 08:09, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O19 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O19 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 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=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TOP3_ECOLI TOP3_ECOLI]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. TOP3 is a potent decatenase.<ref>PMID:2553698</ref> <ref>PMID:6326814</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: DNA topoisomerase]]		[[Category: DNA topoisomerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Changela, A.]]	+	[[Category: Changela, A]]
-	[[Category: DiGate, R.]]	+	[[Category: DiGate, R]]
-	[[Category: Mondragon, A.]]	+	[[Category: Mondragon, A]]
	[[Category: Complex with ssdna]]		[[Category: Complex with ssdna]]
	[[Category: Isomerase-dna complex]]		[[Category: Isomerase-dna complex]]
	[[Category: Topoisomerase]]		[[Category: Topoisomerase]]
	[[Category: Type ia]]		[[Category: Type ia]]

OCA at 03:08, 29 September 2014

2014-09-29T03:08:06Z

←Older revision		Revision as of 03:08, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2o19.~~png~~\|~~left~~\|200px]]	+	==Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5==
		+	<StructureSection load='2o19' size='340' side='right' caption='[[2o19]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2o19]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O19 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1i7d\|1i7d]], [[1d6m\|1d6m]], [[2o54\|2o54]], [[2o59\|2o59]], [[2o5c\|2o5c]], [[2o5e\|2o5e]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">topB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o19 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o19 RCSB], [http://www.ebi.ac.uk/pdbsum/2o19 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o1/2o19_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5' phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.

-	~~{{STRUCTURE_2o19\| PDB=2o19 \| SCENE= }}~~	+	Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate.,Changela A, DiGate RJ, Mondragon A J Mol Biol. 2007 Apr 20;368(1):105-18. Epub 2007 Feb 3. PMID:17331537<ref>PMID:17331537</ref>

-	~~===Structure~~ of E. ~~coli topoisomersae III in complex with an 8-base single stranded oligonucleotide~~. ~~Frozen in glycerol at pH 5~~.~~5===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17331537}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2o19]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA].~~	+

	==See Also==		==See Also==
	*[[Topoisomerase\|Topoisomerase]]		*[[Topoisomerase\|Topoisomerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017331537<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA topoisomerase]]		[[Category: DNA topoisomerase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 05:41, 20 October 2012

2012-10-20T05:41:52Z

←Older revision		Revision as of 05:41, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2o19]] is a 4 chain structure ~~of [[Topoisomerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA].	+	[[2o19]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O19 OCA].

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

OCA at 10:51, 25 July 2012

2012-07-25T10:51:16Z

←Older revision		Revision as of 10:51, 25 July 2012
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	[[Image:2o19.png\|left\|200px]]		[[Image:2o19.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	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_2o19\| PDB=2o19 \| SCENE= }}		{{STRUCTURE_2o19\| PDB=2o19 \| SCENE= }}

	===Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5===		===Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17331537}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17331537 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_17331537}}		{{ABSTRACT_PUBMED_17331537}}

OCA: Protected "2o19" [edit=sysop:move=sysop]

2012-06-10T15:49:08Z

Protected "2o19" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:49, 10 June 2012