2q2e: Difference between revisions

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 ==Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei==
-<StructureSection load='2q2e' size='340' side='right' caption='[[2q2e]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
+<StructureSection load='2q2e' size='340' side='right'caption='[[2q2e]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q2e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q2E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q2e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q2E FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">top6A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053]), top6B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</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]] 4&#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=2q2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2e OCA], [https://pdbe.org/2q2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q2e RCSB], [https://www.ebi.ac.uk/pdbsum/2q2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q2e 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=2q2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q2e OCA], [http://pdbe.org/2q2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q2e RCSB], [http://www.ebi.ac.uk/pdbsum/2q2e PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TOP6A_METMA TOP6A_METMA]] Relaxes both positive and negative superturns and exhibits a strong decatenase activity (By similarity).[HAMAP-Rule:MF_00132] [[http://www.uniprot.org/uniprot/TOP6B_METMA TOP6B_METMA]] Relaxes both positive and negative superturns and exhibits a strong decatenase activity (By similarity).[HAMAP-Rule:MF_00322]
+[https://www.uniprot.org/uniprot/TOP6A_METMA TOP6A_METMA] Relaxes both positive and negative superturns and exhibits a strong decatenase activity (By similarity).[HAMAP-Rule:MF_00132]
 == 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/q2/2q2e_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q2/2q2e_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=2q2e ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Type II topoisomerases help disentangle chromosomes to facilitate cell division. To advance understanding of the structure and dynamics of these essential enzymes, we have determined the crystal structure of an archaeal type IIB topoisomerase, topo VI, at 4.0-A resolution. The 220-kDa heterotetramer adopts a 'twin-gate' architecture, in which a pair of ATPase domains at one end of the enzyme is poised to coordinate DNA movements into the enzyme and through a set of DNA-cleaving domains at the other end. Small-angle X-ray scattering studies show that nucleotide binding elicits a major structural reorganization that is propagated to the enzyme's DNA-cleavage center, explaining how ATP is coupled to DNA capture and strand scission. These data afford important insights into the mechanisms of topo VI and related proteins, including type IIA topoisomerases and the Spo11 meiotic recombination endonuclease.
-Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI.,Corbett KD, Benedetti P, Berger JM Nat Struct Mol Biol. 2007 Jul;14(7):611-9. Epub 2007 Jul 1. PMID:17603498<ref>PMID:17603498</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2q2e" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Topoisomerase|Topoisomerase]]
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
-== References ==
+*[[WD-repeat protein 3D structures|WD-repeat protein 3D structures]]
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Dsm 2053]]
+[[Category: Large Structures]]
-[[Category: Benedetti, P]]
+[[Category: Methanosarcina mazei]]
-[[Category: Berger, J M]]
+[[Category: Benedetti P]]
-[[Category: Corbett, K D]]
+[[Category: Berger JM]]
-[[Category: Atpase]]
+[[Category: Corbett KD]]
-[[Category: Dna-binding]]
-[[Category: Isomerase]]
-[[Category: Spo11]]
-[[Category: Topoisomerase]]