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| | <StructureSection load='2zbk' size='340' side='right'caption='[[2zbk]], [[Resolution|resolution]] 3.56Å' scene=''> | | <StructureSection load='2zbk' size='340' side='right'caption='[[2zbk]], [[Resolution|resolution]] 3.56Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <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> | + | <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> |
| - | </td></tr><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.56Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">top6A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 'Saccharolobus shibatae']), top6B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 'Saccharolobus shibatae'])</td></tr> | + | <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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [https://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=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> | | <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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/TOP6A_SULSH TOP6A_SULSH]] Relaxes both positive and negative superturns and exhibits a strong decatenase activity.[HAMAP-Rule:MF_00132] [[https://www.uniprot.org/uniprot/TOP6B_SULSH TOP6B_SULSH]] Relaxes both positive and negative superturns and exhibits a strong decatenase activity.[HAMAP-Rule:MF_00322]
| + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Saccharolobus shibatae]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cladiere, L]] | + | [[Category: Saccharolobus shibatae]] |
| - | [[Category: Durand, D]] | + | [[Category: Cladiere L]] |
| - | [[Category: Forterre, P]] | + | [[Category: Durand D]] |
| - | [[Category: Graille, M]] | + | [[Category: Forterre P]] |
| - | [[Category: Lecointe, F]] | + | [[Category: Graille M]] |
| - | [[Category: Tilbeurgh, H van]] | + | [[Category: Lecointe F]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Van Tilbeurgh H]] |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Atpase]]
| + | |
| - | [[Category: Decatenation]]
| + | |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Dna topoisomerase]]
| + | |
| - | [[Category: Dna-binding]]
| + | |
| - | [[Category: Drug design]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Ysg]]
| + | |
| Structural highlights
Function
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).[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Buhler C, Lebbink JH, Bocs C, Ladenstein R, Forterre P. DNA topoisomerase VI generates ATP-dependent double-strand breaks with two-nucleotide overhangs. J Biol Chem. 2001 Oct 5;276(40):37215-22. PMID:11485995 doi:10.1074/jbc.M101823200
- ↑ Bergerat A, Gadelle D, Forterre P. Purification of a DNA topoisomerase II from the hyperthermophilic archaeon Sulfolobus shibatae. A thermostable enzyme with both bacterial and eucaryal features. J Biol Chem. 1994 Nov 4;269(44):27663-9 PMID:7961685
- ↑ Graille M, Cladiere L, Durand D, Lecointe F, Gadelle D, Quevillon-Cheruel S, Vachette P, Forterre P, van Tilbeurgh H. Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms. Structure. 2008 Mar;16(3):360-70. PMID:18334211 doi:10.1016/j.str.2007.12.020
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