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| | <StructureSection load='1z59' size='340' side='right'caption='[[1z59]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='1z59' size='340' side='right'caption='[[1z59]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1z59]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'saccharolobus_shibatae' 'saccharolobus shibatae']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z59 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Z59 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1z59]] is a 1 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=1Z59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z59 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mu5|1mu5]], [[1mx0|1mx0]], [[1z5a|1z5a]], [[1z5b|1z5b]], [[1z5c|1z5c]]</div></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=1z59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z59 OCA], [https://pdbe.org/1z59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z59 RCSB], [https://www.ebi.ac.uk/pdbsum/1z59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z59 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">top6B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 'Saccharolobus shibatae'])</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'>[http://proteopedia.org/fgij/fg.htm?mol=1z59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z59 OCA], [http://pdbe.org/1z59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z59 RCSB], [http://www.ebi.ac.uk/pdbsum/1z59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z59 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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/TOP6B_SACSH TOP6B_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: Berger, J M]] | + | [[Category: Saccharolobus shibatae]] |
| - | [[Category: Corbett, K D]] | + | [[Category: Berger JM]] |
| - | [[Category: Archaea]] | + | [[Category: Corbett KD]] |
| - | [[Category: Atpase]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Topoisomerase]]
| + | |
| Structural highlights
Function
TOP6B_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
GHL proteins are functionally diverse enzymes defined by the presence of a conserved ATPase domain that self-associates to trap substrate upon nucleotide binding. The structural states adopted by these enzymes during nucleotide hydrolysis and product release, and their consequences for enzyme catalysis, have remained unclear. Here, we have determined a complete structural map of the ATP turnover cycle for topoVI-B, the ATPase subunit of the archaeal GHL enzyme topoisomerase VI. With this ensemble of structures, we show that significant conformational changes in the subunit occur first upon ATP binding, and subsequently upon release of hydrolyzed P(i). Together, these data provide a structural framework for understanding the role of ATP hydrolysis in the type II topoisomerase reaction. Our results also suggest that the GHL ATPase module is a molecular switch in which ATP hydrolysis serves as a prerequisite but not a driving force for substrate-dependent structural transitions in the enzyme.
Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI.,Corbett KD, Berger JM Structure. 2005 Jun;13(6):873-82. PMID:15939019[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
- ↑ Corbett KD, Berger JM. Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure. 2005 Jun;13(6):873-82. PMID:15939019 doi:http://dx.doi.org/10.1016/j.str.2005.03.013
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