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1kzn

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[[Image:1kzn.gif|left|200px]]<br /><applet load="1kzn" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kzn, resolution 2.30&Aring;" />
 
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'''Crystal Structure of E. coli 24kDa Domain in Complex with Clorobiocin'''<br />
 
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==Overview==
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==Crystal Structure of E. coli 24kDa Domain in Complex with Clorobiocin==
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DNA gyrase is a major bacterial protein that is involved in replication and transcription and catalyzes the negative supercoiling of bacterial circular DNA. DNA gyrase is a known target for antibacterial agents since its blocking induces bacterial death. Quinolones, coumarins, and cyclothialidines have been designed to inhibit gyrase. Significant improvements can still be envisioned for a better coumarin-gyrase interaction. In this work, we obtained the crystal costructures of the natural coumarin clorobiocin and a synthetic analogue with the 24 kDa gyrase fragment. We used isothermal titration microcalorimetry and differential scanning calorimetry to obtain the thermodynamic parameters representative of the molecular interactions occurring during the binding process between coumarins and the 24 kDa gyrase fragment. We provide the first experimental evidence that clorobiocin binds gyrase with a stronger affinity than novobiocin. We also demonstrate the crucial role of both the hydroxybenzoate isopentenyl moiety and the 5'-alkyl group on the noviose of the coumarins in the binding affinity for gyrase.
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<StructureSection load='1kzn' size='340' side='right'caption='[[1kzn]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kzn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KZN 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]] 2.3&#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=CBN:CLOROBIOCIN'>CBN</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=1kzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kzn OCA], [https://pdbe.org/1kzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kzn RCSB], [https://www.ebi.ac.uk/pdbsum/1kzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kzn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GYRB_ECOLI GYRB_ECOLI] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051843</ref> <ref>PMID:18642932</ref> <ref>PMID:20675723</ref>
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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/kz/1kzn_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=1kzn ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KZN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CBN:'>CBN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZN OCA].
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*[[Gyrase 3D Structures|Gyrase 3D Structures]]
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== References ==
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==Reference==
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<references/>
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DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose., Lafitte D, Lamour V, Tsvetkov PO, Makarov AA, Klich M, Deprez P, Moras D, Briand C, Gilli R, Biochemistry. 2002 Jun 11;41(23):7217-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12044152 12044152]
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__TOC__
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[[Category: DNA topoisomerase (ATP-hydrolyzing)]]
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Briand, C.]]
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[[Category: Briand C]]
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[[Category: Deprez, P.]]
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[[Category: Deprez P]]
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[[Category: Gilli, R.]]
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[[Category: Gilli R]]
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[[Category: Klich, M.]]
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[[Category: Klich M]]
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[[Category: Lafitte, D.]]
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[[Category: Lafitte D]]
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[[Category: Lamour, V.]]
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[[Category: Lamour V]]
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[[Category: Makarov, A A.]]
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[[Category: Makarov AA]]
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[[Category: Moras, D.]]
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[[Category: Moras D]]
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[[Category: Tsvetkov, P O.]]
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[[Category: Tsvetkov PO]]
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[[Category: CBN]]
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[[Category: clorobiocin]]
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[[Category: gyrase b]]
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[[Category: topoisomerase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:39:39 2008''
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Current revision

Crystal Structure of E. coli 24kDa Domain in Complex with Clorobiocin

PDB ID 1kzn

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