2q2e: Difference between revisions

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-[[Image:2q2e.jpg|left|200px]]
- {{Structure
+==Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei==
-|PDB= 2q2e |SIZE=350|CAPTION= <scene name='initialview01'>2q2e</scene>, resolution 4.00&Aring;
+<StructureSection load='2q2e' size='340' side='right'caption='[[2q2e]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<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>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4&#8491;</td></tr>
-|GENE= top6A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei]), top6B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])
+<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>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Function ==
-|RESOURCES=<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://www.ebi.ac.uk/pdbsum/2q2e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q2e RCSB]</span>
+[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>
+    <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/main_output.php?pdb_ID=2q2e ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei'''
+==See Also==
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
+*[[WD-repeat protein 3D structures|WD-repeat protein 3D structures]]
-==Overview==
+__TOC__
-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.
+</StructureSection>
+[[Category: Large Structures]]
-==About this Structure==
-Q2E is a [[Protein complex]] structure of sequences from [http://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].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17603498 17603498]
-[[Category: DNA topoisomerase (ATP-hydrolyzing)]]
 [[Category: Methanosarcina mazei]]
-[[Category: Protein complex]]
+[[Category: Benedetti P]]
-[[Category: Benedetti, P.]]
+[[Category: Berger JM]]
-[[Category: Berger, J M.]]
+[[Category: Corbett KD]]
-[[Category: Corbett, K D.]]
-[[Category: atpase]]
-[[Category: dna-binding]]
-[[Category: spo11]]
-[[Category: topoisomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:43:46 2008''