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| | ==Re-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with ADP and SO4== | | ==Re-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with ADP and SO4== |
| - | <StructureSection load='4r1f' size='340' side='right' caption='[[4r1f]], [[Resolution|resolution]] 2.51Å' scene=''> | + | <StructureSection load='4r1f' size='340' side='right'caption='[[4r1f]], [[Resolution|resolution]] 2.51Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4r1f]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R1F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R1F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4r1f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R1F FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.51Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zxn|1zxn]], [[1zxm|1zxm]], [[4prx|4prx]], [[1ei1|1ei1]], [[4pu9|4pu9]], [[4prv|4prv]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4r1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r1f OCA], [https://pdbe.org/4r1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r1f RCSB], [https://www.ebi.ac.uk/pdbsum/4r1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r1f 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=4r1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r1f OCA], [http://pdbe.org/4r1f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r1f RCSB], [http://www.ebi.ac.uk/pdbsum/4r1f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r1f ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TOP2A_HUMAN TOP2A_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Essential during mitosis and meiosis for proper segregation of daughter chromosomes.<ref>PMID:22323612</ref> | + | [https://www.uniprot.org/uniprot/TOP2A_HUMAN TOP2A_HUMAN] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Essential during mitosis and meiosis for proper segregation of daughter chromosomes.<ref>PMID:22323612</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4r1f" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4r1f" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Topoisomerase 3D structures|Topoisomerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Schirmer, T]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Stanger, F V]] | + | [[Category: Large Structures]] |
| - | [[Category: Human topoisomerase iia]] | + | [[Category: Schirmer T]] |
| - | [[Category: Isomerase]] | + | [[Category: Stanger FV]] |
| Structural highlights
Function
TOP2A_HUMAN Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Essential during mitosis and meiosis for proper segregation of daughter chromosomes.[1]
Publication Abstract from PubMed
Type II DNA topoisomerases are essential enzymes that catalyze topological rearrangement of double-stranded DNA using the free energy generated by ATP hydrolysis. Bacterial DNA gyrase is a prototype of this family and is composed of two subunits (GyrA, GyrB) that form a GyrA2GyrB2 heterotetramer. The N-terminal 43-kDa fragment of GyrB (GyrB43) from E. coli comprising the ATPase and the transducer domains has been studied extensively. The dimeric fragment is competent for ATP hydrolysis and its structure in complex with the substrate analog AMPPNP is known. Here, we have determined the remaining conformational states of the enzyme along the ATP hydrolysis reaction path by solving crystal structures of GyrB43 in complex with ADPBeF3, ADPPi, and ADP. Upon hydrolysis, the enzyme undergoes an obligatory 12 degrees domain rearrangement to accommodate the 1.5 A increase in distance between the gamma- and beta-phosphate of the nucleotide within the sealed binding site at the domain interface. Conserved residues from the QTK loop of the transducer domain (also part of the domain interface) couple the small structural change within the binding site with the rigid body motion. The domain reorientation is reflected in a significant 7 A increase in the separation of the two transducer domains of the dimer that would embrace one of the DNA segments in full-length gyrase. The observed conformational change is likely to be relevant for the allosteric coordination of ATP hydrolysis with DNA binding, cleavage/re-ligation and/or strand passage.
Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis.,Stanger FV, Dehio C, Schirmer T PLoS One. 2014 Sep 9;9(9):e107289. doi: 10.1371/journal.pone.0107289. eCollection, 2014. PMID:25202966[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lee S, Jung SR, Heo K, Byl JA, Deweese JE, Osheroff N, Hohng S. DNA cleavage and opening reactions of human topoisomerase IIalpha are regulated via Mg2+-mediated dynamic bending of gate-DNA. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2925-30. doi:, 10.1073/pnas.1115704109. Epub 2012 Feb 9. PMID:22323612 doi:http://dx.doi.org/10.1073/pnas.1115704109
- ↑ Stanger FV, Dehio C, Schirmer T. Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis. PLoS One. 2014 Sep 9;9(9):e107289. doi: 10.1371/journal.pone.0107289. eCollection, 2014. PMID:25202966 doi:http://dx.doi.org/10.1371/journal.pone.0107289
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