1kij

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(New page: 200px<br /><applet load="1kij" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kij, resolution 2.30&Aring;" /> '''Crystal structure of...)
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[[Image:1kij.gif|left|200px]]<br /><applet load="1kij" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kij, resolution 2.30&Aring;" />
 
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'''Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin'''<br />
 
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==Overview==
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==Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin==
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DNA gyrase forms an A(2)B(2) tetramer involved in DNA replication, repair, recombination, and transcription in which the B subunit catalyzes ATP, hydrolysis. The Thermus thermophilus and Escherichia coli gyrases are, homologues and present the same catalytic activity. When compared with, that of the E. coli 43K-5'-adenylyl-beta,gamma-imidodiphosphate complex, the crystal structure of Gyrase B 43K ATPase domain in complex with, novobiocin, one of the most potent inhibitors of gyrase shows large, conformational changes of the subdomains within the dimer. The, stabilization of loop 98-118 closing the active site through dimeric, contacts and interaction with domain 2 allows to observe, novobiocin-protein interactions that could not be seen in the, 24K-inhibitor complexes. Furthermore, this loop adopts a position which, defines an "open" conformation of the active site in absence of ATP, in, contrast with the "closed" conformation adopted upon ATP binding. All, together, these results indicate how the subdomains may propagate, conformational changes from the active site and provide crucial, information for the design of more specific inhibitors.
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<StructureSection load='1kij' size='340' side='right'caption='[[1kij]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kij]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KIJ 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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NOV:NOVOBIOCIN'>NOV</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=1kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kij OCA], [https://pdbe.org/1kij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kij RCSB], [https://www.ebi.ac.uk/pdbsum/1kij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kij ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GYRB_THET8 GYRB_THET8] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:23804759, PubMed:11850422). It probably also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:11850422). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:23804759, PubMed:11850422). At comparable concentrations T.thermophilus gyrase does not introduce as many negative supercoils into DNA as the E.coli enzyme (PubMed:23804759).<ref>PMID:23804759</ref> Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.
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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/ki/1kij_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=1kij 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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1KIJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with NOV and FMT as [http://en.wikipedia.org/wiki/ligands ligands]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KIJ 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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An open conformation of the Thermus thermophilus gyrase B ATP-binding domain., Lamour V, Hoermann L, Jeltsch JM, Oudet P, Moras D, J Biol Chem. 2002 May 24;277(21):18947-53. Epub 2002 Feb 15. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11850422 11850422]
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__TOC__
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[[Category: DNA topoisomerase (ATP-hydrolyzing)]]
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</StructureSection>
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[[Category: Single protein]]
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[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Hoermann, L.]]
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[[Category: Hoermann L]]
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[[Category: Jeltsch, J.M.]]
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[[Category: Jeltsch J-M]]
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[[Category: Lamour, V.]]
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[[Category: Lamour V]]
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[[Category: Moras, D.]]
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[[Category: Moras D]]
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[[Category: Oudet, P.]]
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[[Category: Oudet P]]
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[[Category: FMT]]
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[[Category: NOV]]
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[[Category: gyrase b-coumarin complex]]
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[[Category: topoisomerase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:25:09 2007''
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Current revision

Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin

PDB ID 1kij

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