2y3p

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[[Image:2y3p.png|left|200px]]
 
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==Crystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8==
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The line below this paragraph, containing "STRUCTURE_2y3p", creates the "Structure Box" on the page.
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<StructureSection load='2y3p' size='340' side='right'caption='[[2y3p]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2y3p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2wl2 2wl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y3P 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]] 2.62&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SM8:SIMOCYCLINONE+D8'>SM8</scene></td></tr>
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{{STRUCTURE_2y3p| PDB=2y3p | SCENE= }}
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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=2y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y3p OCA], [https://pdbe.org/2y3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y3p RCSB], [https://www.ebi.ac.uk/pdbsum/2y3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y3p ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GYRA_SHIFL GYRA_SHIFL] 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 (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.
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===CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF GYRA WITH THE ANTIBIOTIC SIMOCYCLINONE D8===
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A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.,Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CE, Le TB, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A Science. 2009 Dec 4;326(5958):1415-8. PMID:19965760<ref>PMID:19965760</ref>
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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 class="pdbe-citations 2y3p" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19965760 is the PubMed ID number.
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{{ABSTRACT_PUBMED_19965760}}
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==About this Structure==
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[[2y3p]] is a 2 chain structure of [[Gyrase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2wl2 2wl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y3P OCA].
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==See Also==
==See Also==
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*[[Gyrase]]
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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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<ref group="xtra">PMID:19965760</ref><ref group="xtra">PMID:19652356</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Buttner, M J.]]
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[[Category: Large Structures]]
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[[Category: Clarke, T A.]]
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[[Category: Buttner MJ]]
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[[Category: Edwards, M J.]]
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[[Category: Clarke TA]]
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[[Category: Fiedler, H P.]]
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[[Category: Edwards MJ]]
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[[Category: Flatman, R H.]]
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[[Category: Fiedler H-P]]
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[[Category: Lawson, D M.]]
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[[Category: Flatman RH]]
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[[Category: Le, T B.K.]]
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[[Category: Lawson DM]]
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[[Category: Maxwell, A.]]
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[[Category: Le TBK]]
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[[Category: Mckay, A R.]]
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[[Category: Maxwell A]]
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[[Category: Mitchenall, L A.]]
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[[Category: McKay AR]]
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[[Category: Stevenson, C E.M.]]
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[[Category: Mitchenall LA]]
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[[Category: Aminocoumarin antibiotic]]
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[[Category: Stevenson CEM]]
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[[Category: Isomerase]]
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Current revision

Crystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8

PDB ID 2y3p

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