2zbk

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[[Image:2zbk.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms==
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|PDB= 2zbk |SIZE=350|CAPTION= <scene name='initialview01'>2zbk</scene>, resolution 3.560&Aring;
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<StructureSection load='2zbk' size='340' side='right'caption='[[2zbk]], [[Resolution|resolution]] 3.56&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Rdc+Binding+Site+For+Residue+B+531'>AC1</scene>, <scene name='pdbsite=AC2:Rdc+Binding+Site+For+Residue+D+531'>AC2</scene>, <scene name='pdbsite=AC3:Rdc+Binding+Site+For+Residue+F+531'>AC3</scene> and <scene name='pdbsite=AC4:Rdc+Binding+Site+For+Residue+H+531'>AC4</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=RDC:RADICICOL'>RDC</scene>
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<table><tr><td colspan='2'>[[2zbk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_shibatae Saccharolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZBK FirstGlance]. <br>
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|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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.56&#8491;</td></tr>
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|GENE= top6A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 Sulfolobus shibatae]), top6B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 Sulfolobus shibatae])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RDC:RADICICOL'>RDC</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbk OCA], [https://pdbe.org/2zbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zbk RCSB], [https://www.ebi.ac.uk/pdbsum/2zbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zbk ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbk OCA], [http://www.ebi.ac.uk/pdbsum/2zbk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2zbk RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/TOP6A_SACSH TOP6A_SACSH] Relaxes both positive and negative supercoils and exhibits a strong decatenase and unknotting activity; it cannot introduce DNA supercoils (PubMed:7961685). ATP is absolutely required for DNA cleavage; the nonhydrolyzable analog AMP-PNP generates nicked or linear products from a supercoiled dsDNA substrate. Generates staggered two-nucleotide long 5' overhangs. The enzyme is covalently attached transiently to the 5'-ends of the cleaved strands (PubMed:11485995).<ref>PMID:11485995</ref> <ref>PMID:7961685</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zb/2zbk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2zbk ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA topoisomerases resolve DNA topological problems created during transcription, replication, and recombination. These ubiquitous enzymes are essential for cell viability and are highly potent targets for the development of antibacterial and antitumoral drugs. Type II enzymes catalyze the transfer of a DNA duplex through another one in an ATP-dependent mechanism. Because of its small size and sensitivity to antitumoral drugs, the archaeal DNA topoisomerase VI, a type II enzyme, is an excellent model for gaining further understanding of the organization and mechanism of these enzymes. We present the crystal structure of intact DNA topoisomerase VI bound to radicicol, an inhibitor of human topo II, and compare it to the conformation of the apo-protein as determined by small-angle X-ray scattering in solution. This structure, combined with a wealth of experimental data gathered on these enzymes, allows us to propose a structural model for the two-gate DNA transfer mechanism.
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'''Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms'''
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Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms.,Graille M, Cladiere L, Durand D, Lecointe F, Gadelle D, Quevillon-Cheruel S, Vachette P, Forterre P, van Tilbeurgh H Structure. 2008 Mar;16(3):360-70. PMID:18334211<ref>PMID:18334211</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2zbk" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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2ZBK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sulfolobus_shibatae Sulfolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBK OCA].
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*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
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[[Category: DNA topoisomerase (ATP-hydrolyzing)]]
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== References ==
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[[Category: Protein complex]]
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<references/>
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[[Category: Sulfolobus shibatae]]
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__TOC__
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[[Category: Cladiere, L.]]
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</StructureSection>
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[[Category: Durand, D.]]
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[[Category: Large Structures]]
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[[Category: Forterre, P.]]
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[[Category: Saccharolobus shibatae]]
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[[Category: Graille, M.]]
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[[Category: Cladiere L]]
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[[Category: Lecointe, F.]]
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[[Category: Durand D]]
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[[Category: Tilbeurgh, H van.]]
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[[Category: Forterre P]]
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[[Category: atp-binding]]
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[[Category: Graille M]]
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[[Category: atpase]]
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[[Category: Lecointe F]]
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[[Category: decatenation]]
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[[Category: Van Tilbeurgh H]]
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[[Category: dna binding protein]]
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[[Category: dna topoisomerase]]
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[[Category: dna-binding]]
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[[Category: drug design]]
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[[Category: magnesium]]
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[[Category: metal-binding]]
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[[Category: nucleotide-binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:20:11 2008''
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Current revision

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

PDB ID 2zbk

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