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| | <StructureSection load='3l4j' size='340' side='right'caption='[[3l4j]], [[Resolution|resolution]] 2.48Å' scene=''> | | <StructureSection load='3l4j' size='340' side='right'caption='[[3l4j]], [[Resolution|resolution]] 2.48Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3l4j]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L4J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3l4j]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L4J FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TSP:3-THIO-THYMIDINE-5-PHOSPHATE'>TSP</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]] 2.48Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene>, <scene name='pdbligand=TSP:3-THIO-THYMIDINE-5-PHOSPHATE'>TSP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3l4k|3l4k]]</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=3l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l4j OCA], [https://pdbe.org/3l4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l4j RCSB], [https://www.ebi.ac.uk/pdbsum/3l4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l4j ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">N2244, TOP2, TOR3, YNL088W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l4j OCA], [http://pdbe.org/3l4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l4j RCSB], [http://www.ebi.ac.uk/pdbsum/3l4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l4j ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TOP2_YEAST TOP2_YEAST]] 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:9685374</ref> <ref>PMID:23022727</ref> | + | [https://www.uniprot.org/uniprot/TOP2_YEAST TOP2_YEAST] 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:9685374</ref> <ref>PMID:23022727</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Topoisomerase|Topoisomerase]] | + | *[[Topoisomerase 3D structures|Topoisomerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Berger, J M]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Burgin, A B]] | + | [[Category: Berger JM]] |
| - | [[Category: Deweese, J E]] | + | [[Category: Burgin AB]] |
| - | [[Category: Osheroff, N]] | + | [[Category: Deweese JE]] |
| - | [[Category: Schmidt, B H]] | + | [[Category: Osheroff N]] |
| - | [[Category: Atp-binding]] | + | [[Category: Schmidt BH]] |
| - | [[Category: Covalently linked complex]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Dna supercoiling]]
| + | |
| - | [[Category: Dna-binding]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Isomerase-dna complex]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Nucleus]]
| + | |
| - | [[Category: Phosphoprotein]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Topoisomerase]]
| + | |
| Structural highlights
Function
TOP2_YEAST 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] [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
Type II topoisomerases are required for the management of DNA tangles and supercoils, and are targets of clinical antibiotics and anti-cancer agents. These enzymes catalyse the ATP-dependent passage of one DNA duplex (the transport or T-segment) through a transient, double-stranded break in another (the gate or G-segment), navigating DNA through the protein using a set of dissociable internal interfaces, or 'gates'. For more than 20 years, it has been established that a pair of dimer-related tyrosines, together with divalent cations, catalyse G-segment cleavage. Recent efforts have proposed that strand scission relies on a 'two-metal mechanism', a ubiquitous biochemical strategy that supports vital cellular processes ranging from DNA synthesis to RNA self-splicing. Here we present the structure of the DNA-binding and cleavage core of Saccharomyces cerevisiae topoisomerase II covalently linked to DNA through its active-site tyrosine at 2.5A resolution, revealing for the first time the organization of a cleavage-competent type II topoisomerase configuration. Unexpectedly, metal-soaking experiments indicate that cleavage is catalysed by a novel variation of the classic two-metal approach. Comparative analyses extend this scheme to explain how distantly-related type IA topoisomerases cleave single-stranded DNA, unifying the cleavage mechanisms for these two essential enzyme families. The structure also highlights a hitherto undiscovered allosteric relay that actuates a molecular 'trapdoor' to prevent subunit dissociation during cleavage. This connection illustrates how an indispensable chromosome-disentangling machine auto-regulates DNA breakage to prevent the aberrant formation of mutagenic and cytotoxic genomic lesions.
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.,Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM Nature. 2010 Jun 3;465(7298):641-4. PMID:20485342[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Liu Q, Wang JC. Identification of active site residues in the "GyrA" half of yeast DNA topoisomerase II. J Biol Chem. 1998 Aug 7;273(32):20252-60. PMID:9685374
- ↑ Schmidt BH, Osheroff N, Berger JM. Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nat Struct Mol Biol. 2012 Nov;19(11):1147-54. doi: 10.1038/nsmb.2388. Epub 2012, Sep 30. PMID:23022727 doi:http://dx.doi.org/10.1038/nsmb.2388
- ↑ Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM. A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature. 2010 Jun 3;465(7298):641-4. PMID:20485342 doi:10.1038/nature08974
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