3m4a

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{{STRUCTURE_3m4a| PDB=3m4a | SCENE= }}
 
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===Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site===
 
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{{ABSTRACT_PUBMED_20541510}}
 
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==About this Structure==
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==Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site==
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[[3m4a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M4A OCA].
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<StructureSection load='3m4a' size='340' side='right'caption='[[3m4a]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3m4a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M4A FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3m4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m4a OCA], [https://pdbe.org/3m4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m4a RCSB], [https://www.ebi.ac.uk/pdbsum/3m4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m4a ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9RWH8_DEIRA Q9RWH8_DEIRA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m4/3m4a_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3m4a ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Type IB DNA topoisomerases (TopIB) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex DNA within a protein clamp that embraces a approximately 21 DNA segment. A longstanding conundrum concerns the capacity of TopIB enzymes to stabilize intramolecular duplex DNA crossovers and form protein-DNA synaptic filaments. Here we report a structure of Deinococcus radiodurans TopIB in complex with a 12 bp duplex DNA that demonstrates a secondary DNA binding site located on the surface of the C-terminal domain. It comprises a distinctive interface with one strand of the DNA duplex and is conserved in all TopIB enzymes. Modeling of a TopIB with both DNA sites suggests that the secondary site could account for DNA crossover binding, nucleation of DNA synapsis, and generation of a filamentous plectoneme. Mutations of the secondary site eliminate synaptic plectoneme formation without affecting DNA cleavage or supercoil relaxation.
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==Reference==
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Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.,Patel A, Yakovleva L, Shuman S, Mondragon A Structure. 2010 Jun 9;18(6):725-33. PMID:20541510<ref>PMID:20541510</ref>
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<ref group="xtra">PMID:020541510</ref><references group="xtra"/><references/>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3m4a" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Mondragon, A.]]
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[[Category: Large Structures]]
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[[Category: Patel, A.]]
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[[Category: Mondragon A]]
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[[Category: Shuman, S.]]
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[[Category: Patel A]]
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[[Category: Yakovleva, L.]]
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[[Category: Shuman S]]
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[[Category: Isomerase-dna complex]]
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[[Category: Yakovleva L]]
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[[Category: Protein-dna complex]]
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[[Category: Topib]]
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[[Category: Type ib]]
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Current revision

Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site

PDB ID 3m4a

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