4vub - Revision history

OCA at 12:59, 1 March 2024

2024-03-01T12:59:10Z

←Older revision		Revision as of 12:59, 1 March 2024
Line 1:		Line 1:

	==CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI==		==CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI==
-	<StructureSection load='4vub' size='340' side='right' caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='4vub' size='340' side='right'caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4VUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4VUB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.45Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CCDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [~~http~~://pdbe.org/4vub PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4vub PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4vub 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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [https://pdbe.org/4vub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [https://www.ebi.ac.uk/pdbsum/4vub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4vub ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CCDB_ECOLI CCDB_ECOLI]] Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.<ref>PMID:6327993</ref> <ref>PMID:2651399</ref> <ref>PMID:6308648</ref> <ref>PMID:2615761</ref> <ref>PMID:1324324</ref> <ref>PMID:8604132</ref>	+	[https://www.uniprot.org/uniprot/CCDB_ECOLI CCDB_ECOLI] Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.<ref>PMID:6327993</ref> <ref>PMID:2651399</ref> <ref>PMID:6308648</ref> <ref>PMID:2615761</ref> <ref>PMID:1324324</ref> <ref>PMID:8604132</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=4vub 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=4vub ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of CcdB, a protein that poisons Escherichia coli gyrase, was determined in three crystal forms. The protein consists of a five-stranded antiparallel beta-pleated sheet followed by a C-terminal alpha-helix. In one of the loops of the sheet, a second small three-stranded antiparallel beta-sheet is inserted that sticks out of the molecule as a wing. This wing contains the LysC proteolytic cleavage site that is protected by CcdA and, therefore, forms a likely CcdA recognition site. A dimer is formed by sheet extension and by extensive hydrophobic contacts involving three of the five methionine residues and the C terminus of the alpha-helix. The surface of the dimer on the side of the alpha-helix is overall negatively charged, while the opposite side as well as the wing sheet is dominated by positive charges. We propose that the CcdB dimer binds into the central hole of the 59 kDa N-terminal fragment of GyrA, after disruption of the head dimer interface of GyrA.
-
-	Crystal structure of CcdB, a topoisomerase poison from E. coli.,Loris R, Dao-Thi MH, Bahassi EM, Van Melderen L, Poortmans F, Liddington R, Couturier M, Wyns L J Mol Biol. 1999 Jan 29;285(4):1667-77. PMID:9917404<ref>PMID:9917404</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4vub" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: Bahasi~~, E M~~]]	+	[[Category: Large Structures]]
-	[[Category: Couturier, M]]	+	[[Category: Bahasi EM]]
-	[[Category: Dao-Thi, M H]]	+	[[Category: Couturier M]]
-	[[Category: Liddington, R]]	+	[[Category: Dao-Thi M-H]]
-	[[Category: Loris, R]]	+	[[Category: Liddington R]]
-	~~[[Category: Melderen, L Van~~]]	+	[[Category: Loris R]]
-	[[Category: Poortmans, F]]	+	[[Category: Poortmans F]]
-	[[Category: ~~Wyns,~~ L]]	+	[[Category: Van Melderen L]]
-	[[Category: ~~Ccdb]]~~	+	[[Category: Wyns L]]
-	~~[[Category: Plasmid]]~~	+
-	~~[[Category: Plasmid addiction]]~~	+
-	~~[[Category: Topoisomerase poison~~]]	+

OCA at 06:12, 18 April 2018

2018-04-18T06:12:31Z

←Older revision		Revision as of 06:12, 18 April 2018
Line 1:		Line 1:
		+
	==CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI==		==CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI==
	<StructureSection load='4vub' size='340' side='right' caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='4vub' size='340' side='right' caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCDB ([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">CCDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://pdbe.org/4vub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub 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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://pdbe.org/4vub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4vub ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vu/4vub_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vu/4vub_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 42:		Line 43:
	[[Category: Wyns, L]]		[[Category: Wyns, L]]
	[[Category: Ccdb]]		[[Category: Ccdb]]
		+	[[Category: Plasmid]]
	[[Category: Plasmid addiction]]		[[Category: Plasmid addiction]]
	[[Category: Topoisomerase poison]]		[[Category: Topoisomerase poison]]

OCA at 10:19, 8 February 2016

2016-02-08T10:19:55Z

←Older revision		Revision as of 10:19, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='4vub' size='340' side='right' caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='4vub' size='340' side='right' caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4VUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4VUB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCDB ([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">CCDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub 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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://pdbe.org/4vub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<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=4vub ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 4vub" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Bahasi, E M]]		[[Category: Bahasi, E M]]
	[[Category: Couturier, M]]		[[Category: Couturier, M]]

OCA at 22:38, 24 December 2014

2014-12-24T22:38:30Z

←Older revision		Revision as of 22:38, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4VUB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4VUB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCDB ([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">CCDB ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub 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=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CCDB_ECOLI CCDB_ECOLI]] Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.<ref>PMID:6327993</ref> <ref>PMID:2651399</ref> <ref>PMID:6308648</ref> <ref>PMID:2615761</ref> <ref>PMID:1324324</ref> <ref>PMID:8604132</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Bahasi, E M.]]	+	[[Category: Bahasi, E M]]
-	[[Category: Couturier, M.]]	+	[[Category: Couturier, M]]
-	[[Category: Dao-Thi, M H.]]	+	[[Category: Dao-Thi, M H]]
-	[[Category: Liddington, R.]]	+	[[Category: Liddington, R]]
-	[[Category: Loris, R.]]	+	[[Category: Loris, R]]
-	[[Category: Melderen, L Van.]]	+	[[Category: Melderen, L Van]]
-	[[Category: Poortmans, F.]]	+	[[Category: Poortmans, F]]
-	[[Category: Wyns, L.]]	+	[[Category: Wyns, L]]
	[[Category: Ccdb]]		[[Category: Ccdb]]
	[[Category: Plasmid addiction]]		[[Category: Plasmid addiction]]
	[[Category: Topoisomerase poison]]		[[Category: Topoisomerase poison]]

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

2014-06-05T08:30:38Z

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

←Older revision

Revision as of 08:30, 5 June 2014

OCA at 08:30, 5 June 2014

2014-06-05T08:30:37Z

←Older revision		Revision as of 08:30, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI==
-	[[~~Image:~~4vub.~~png~~\|~~left~~\|200px]]	+	<StructureSection load='4vub' size='340' side='right' caption='[[4vub]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4vub]] is a 1 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=4VUB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4VUB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCDB ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB], [http://www.ebi.ac.uk/pdbsum/4vub 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/vu/4vub_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 ==
		+	The crystal structure of CcdB, a protein that poisons Escherichia coli gyrase, was determined in three crystal forms. The protein consists of a five-stranded antiparallel beta-pleated sheet followed by a C-terminal alpha-helix. In one of the loops of the sheet, a second small three-stranded antiparallel beta-sheet is inserted that sticks out of the molecule as a wing. This wing contains the LysC proteolytic cleavage site that is protected by CcdA and, therefore, forms a likely CcdA recognition site. A dimer is formed by sheet extension and by extensive hydrophobic contacts involving three of the five methionine residues and the C terminus of the alpha-helix. The surface of the dimer on the side of the alpha-helix is overall negatively charged, while the opposite side as well as the wing sheet is dominated by positive charges. We propose that the CcdB dimer binds into the central hole of the 59 kDa N-terminal fragment of GyrA, after disruption of the head dimer interface of GyrA.

-	<!--	+	Crystal structure of CcdB, a topoisomerase poison from E. coli.,Loris R, Dao-Thi MH, Bahassi EM, Van Melderen L, Poortmans F, Liddington R, Couturier M, Wyns L J Mol Biol. 1999 Jan 29;285(4):1667-77. PMID:9917404<ref>PMID:9917404</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_4vub"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~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.~~	+
-	-->	+
-	~~{{STRUCTURE_4vub\| PDB=4vub \| SCENE= }}~~	+

-	~~===CCDB~~, ~~A TOPOISOMERASE POISON FROM ESCHERICHIA COLI===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_9917404}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 9917404 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_9917404}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~4VUB is a 1 chain structure of 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=4VUB OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:9917404<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Bahasi, E M.]]		[[Category: Bahasi, E M.]]
Line 34:		Line 39:
	[[Category: Wyns, L.]]		[[Category: Wyns, L.]]
	[[Category: Ccdb]]		[[Category: Ccdb]]
-	[[Category: Plasmid]]
	[[Category: Plasmid addiction]]		[[Category: Plasmid addiction]]
	[[Category: Topoisomerase poison]]		[[Category: Topoisomerase poison]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:17:14 2009''

OCA at 19:17, 16 February 2009

2009-02-16T19:17:15Z

←Older revision		Revision as of 19:17, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	4VUB is a ~~[[Single protein]]~~ structure of 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=4VUB OCA].	+	4VUB is a 1 chain structure of 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=4VUB OCA].

	==Reference==		==Reference==
-	Crystal structure of CcdB, a topoisomerase poison from E. coli., Loris R, Dao-Thi MH, Bahassi EM, Van Melderen L, Poortmans F, Liddington R, Couturier M, Wyns L, J Mol Biol. 1999 Jan 29;285(4):1667-77. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9917404 9917404]~~	+	<ref group="xtra">PMID:9917404</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Bahasi, E M.]]		[[Category: Bahasi, E M.]]
	[[Category: Couturier, M.]]		[[Category: Couturier, M.]]
Line 39:		Line 38:
	[[Category: Topoisomerase poison]]		[[Category: Topoisomerase poison]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 13~~:54:~~26 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:17:14 2009''

OCA at 10:54, 3 July 2008

2008-07-03T10:54:27Z

←Older revision		Revision as of 10:54, 3 July 2008
Line 1:		Line 1:
-	[[Image:4vub.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:4vub.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_4vub\| PDB=4vub \| SCENE= }}		{{STRUCTURE_4vub\| PDB=4vub \| SCENE= }}

-	~~'''~~CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI~~'''~~	+	===CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI===


-	~~==Overview==~~	+	<!--
-	The ~~crystal structure of CcdB~~, ~~a protein that poisons Escherichia coli gyrase~~, ~~was determined in three crystal forms. The protein consists of a five-stranded antiparallel beta-pleated sheet followed by a C-terminal alpha-helix. In one of~~ the ~~loops of~~ the ~~sheet, a second small three-stranded antiparallel beta-sheet is inserted that sticks out of the molecule~~ as ~~a wing~~. ~~This wing contains the LysC proteolytic cleavage site that is protected by CcdA and~~, ~~therefore, forms a likely CcdA recognition site. A dimer~~ is ~~formed by sheet extension and by extensive hydrophobic contacts involving three of~~ the ~~five methionine residues and the C terminus of the alpha-helix~~. ~~The surface of the dimer on the side of the alpha~~-~~helix is overall negatively charged, while the opposite side as well as the wing sheet is dominated by positive charges. We propose that the CcdB dimer binds into the central hole of the 59 kDa N~~-~~terminal fragment of GyrA, after disruption of the head dimer interface of GyrA.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9917404}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9917404 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9917404}}

	==About this Structure==		==About this Structure==
Line 34:		Line 38:
	[[Category: Plasmid addiction]]		[[Category: Plasmid addiction]]
	[[Category: Topoisomerase poison]]		[[Category: Topoisomerase poison]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:31:09 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:54:26 2008''

OCA at 19:31, 4 May 2008

2008-05-04T19:31:11Z

←Older revision		Revision as of 19:31, 4 May 2008
Line 1:		Line 1:
	[[Image:4vub.gif\|left\|200px]]		[[Image:4vub.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 4vub \|SIZE=350\|CAPTION= <scene name='initialview01'>4vub</scene>~~, ~~resolution 1~~.~~45Å~~	+	The line below this paragraph, containing "STRUCTURE_4vub", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY=~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= CCDB ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])~~	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_4vub\| PDB=4vub \| SCENE= }}
-	\|~~RELATEDENTRY~~=	+
-	\|~~RESOURCES~~=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://www.ebi.ac.uk/pdbsum/4vub PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB]</span>	+
-	}}	+

	'''CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI'''		'''CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI'''
Line 33:		Line 30:
	[[Category: Poortmans, F.]]		[[Category: Poortmans, F.]]
	[[Category: Wyns, L.]]		[[Category: Wyns, L.]]
-	[[Category: ~~ccdb~~]]	+	[[Category: Ccdb]]
-	[[Category: ~~plasmid~~]]	+	[[Category: Plasmid]]
-	[[Category: ~~plasmid~~ addiction]]	+	[[Category: Plasmid addiction]]
-	[[Category: ~~topoisomerase~~ poison]]	+	[[Category: Topoisomerase poison]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:31:09 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:40:38 2008''	+

OCA at 02:40, 31 March 2008

2008-03-31T02:40:39Z

←Older revision		Revision as of 02:40, 31 March 2008
Line 4:		Line 4:
	\|PDB= 4vub \|SIZE=350\|CAPTION= <scene name='initialview01'>4vub</scene>, resolution 1.45Å		\|PDB= 4vub \|SIZE=350\|CAPTION= <scene name='initialview01'>4vub</scene>, resolution 1.45Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene>	+	\|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE= CCDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])		\|GENE= CCDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4vub OCA], [http://www.ebi.ac.uk/pdbsum/4vub PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4vub RCSB]</span>
	}}		}}

Line 30:		Line 33:
	[[Category: Poortmans, F.]]		[[Category: Poortmans, F.]]
	[[Category: Wyns, L.]]		[[Category: Wyns, L.]]
-	[[Category: CL]]
	[[Category: ccdb]]		[[Category: ccdb]]
	[[Category: plasmid]]		[[Category: plasmid]]
Line 36:		Line 38:
	[[Category: topoisomerase poison]]		[[Category: topoisomerase poison]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:11:22 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:40:38 2008''