2o5c
From Proteopedia
(Difference between revisions)
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==Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5== | ==Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5== | ||
| - | <StructureSection load='2o5c' size='340' side='right' caption='[[2o5c]], [[Resolution|resolution]] 2.35Å' scene=''> | + | <StructureSection load='2o5c' size='340' side='right'caption='[[2o5c]], [[Resolution|resolution]] 2.35Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2o5c]] is a 4 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2o5c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O5C FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1i7d|1i7d]], [[1d6m|1d6m]], [[2o54|2o54]], [[2o59|2o59]], [[2o5e|2o5e]], [[2o19|2o19]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i7d|1i7d]], [[1d6m|1d6m]], [[2o54|2o54]], [[2o59|2o59]], [[2o5e|2o5e]], [[2o19|2o19]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">topB ([ | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">topB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5c OCA], [https://pdbe.org/2o5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o5c RCSB], [https://www.ebi.ac.uk/pdbsum/2o5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5c ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [[ | + | [[https://www.uniprot.org/uniprot/TOP3_ECOLI TOP3_ECOLI]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. TOP3 is a potent decatenase.<ref>PMID:2553698</ref> <ref>PMID:6326814</ref> |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o5/2o5c_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o5/2o5c_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2o5c" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2o5c" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Topoisomerase 3D structures|Topoisomerase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Bacillus coli migula 1895]] | [[Category: Bacillus coli migula 1895]] | ||
[[Category: DNA topoisomerase]] | [[Category: DNA topoisomerase]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Changela, A]] | [[Category: Changela, A]] | ||
[[Category: DiGate, R J]] | [[Category: DiGate, R J]] | ||
Revision as of 16:00, 8 June 2021
Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5
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