1x75: Difference between revisions

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 ==CcdB:GyrA14 complex==
-<StructureSection load='1x75' size='340' side='right' caption='[[1x75]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1x75' size='340' side='right'caption='[[1x75]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1x75]] 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=1X75 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X75 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1x75]] 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=1X75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X75 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ab4|1ab4]], [[1vub|1vub]], [[2vub|2vub]], [[3vub|3vub]], [[4vub|4vub]]</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]] 2.8&#8491;</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=1x75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x75 OCA], [https://pdbe.org/1x75 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x75 RCSB], [https://www.ebi.ac.uk/pdbsum/1x75 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x75 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=1x75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x75 OCA], [http://pdbe.org/1x75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x75 RCSB], [http://www.ebi.ac.uk/pdbsum/1x75 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GYRA_ECOLI GYRA_ECOLI]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051842</ref> <ref>PMID:18642932</ref> <ref>PMID:19965760</ref>  [[http://www.uniprot.org/uniprot/CCDB_ECO57 CCDB_ECO57]] 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. 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. 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. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA (By similarity).
+[https://www.uniprot.org/uniprot/GYRA_ECOLI GYRA_ECOLI] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051842</ref> <ref>PMID:18642932</ref> <ref>PMID:19965760</ref>
 == 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/x7/1x75_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x7/1x75_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 19: @@
 </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=1x75 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Gyrase is an ubiquitous bacterial enzyme that is responsible for disentangling DNA during DNA replication and transcription. It is the target of the toxin CcdB, a paradigm for plasmid addiction systems and related bacterial toxin-antitoxin systems. The crystal structure of CcdB and the dimerization domain of the A subunit of gyrase (GyrA14) dictates an open conformation for the catalytic domain of gyrase when CcdB is bound. The action of CcdB is one of a wedge that stabilizes a dead-end covalent gyrase:DNA adduct. Although CcdB and GyrA14 form a globally symmetric complex where the two 2-fold axes of both dimers align, the complex is asymmetric in its details. At the centre of the interaction site, the Trp99 pair of CcdB stacks with the Arg462 pair of GyrA14, explaining why the Arg462Cys mutation in the A subunit of gyrase confers resistance to CcdB. Overexpression of GyrA14 protects Escherichia coli cells against CcdB, mimicking the action of the antidote CcdA.
-Molecular basis of gyrase poisoning by the addiction toxin CcdB.,Dao-Thi MH, Van Melderen L, De Genst E, Afif H, Buts L, Wyns L, Loris R J Mol Biol. 2005 May 20;348(5):1091-102. Epub 2005 Apr 7. PMID:15854646<ref>PMID:15854646</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1x75" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Gyrase|Gyrase]]
+*[[Gyrase 3D Structures|Gyrase 3D Structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Dao-Thi, M H]]
+[[Category: Large Structures]]
-[[Category: Genst, E De]]
+[[Category: Dao-Thi MH]]
-[[Category: Loris, R]]
+[[Category: De Genst E]]
-[[Category: Melderen, L Van]]
+[[Category: Loris R]]
-[[Category: Wyns, L]]
+[[Category: Van Melderen L]]
-[[Category: Bacterial cell death]]
+[[Category: Wyns L]]
-[[Category: Ccdb]]
-[[Category: Gyrase]]
-[[Category: Isomerase-signaling protein complex]]
-[[Category: Plasmid addiction]]
-[[Category: Ta system]]
-[[Category: Topoisomerase]]