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| | <StructureSection load='6qx2' size='340' side='right'caption='[[6qx2]], [[Resolution|resolution]] 3.40Å' scene=''> | | <StructureSection load='6qx2' size='340' side='right'caption='[[6qx2]], [[Resolution|resolution]] 3.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6qx2]] is a 36 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QX2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QX2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6qx2]] is a 34 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QX2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QX2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JK8:(2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine'>JK8</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6qx1|6qx1]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JK8:(2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine'>JK8</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6qx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qx2 OCA], [https://pdbe.org/6qx2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qx2 RCSB], [https://www.ebi.ac.uk/pdbsum/6qx2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qx2 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6qx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qx2 OCA], [http://pdbe.org/6qx2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qx2 RCSB], [http://www.ebi.ac.uk/pdbsum/6qx2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qx2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GYRB_STAAN GYRB_STAAN]] 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). [[http://www.uniprot.org/uniprot/GYRA_STAAN GYRA_STAAN]] 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.[HAMAP-Rule:MF_01897] [[http://www.uniprot.org/uniprot/GYRB_STAAU GYRB_STAAU]] 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.[HAMAP-Rule:MF_01898] | + | [https://www.uniprot.org/uniprot/GYRB_STAAU GYRB_STAAU] 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.[HAMAP-Rule:MF_01898] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6qx2" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6qx2" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Gyrase 3D Structures|Gyrase 3D Structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bax, B D]] | + | [[Category: Staphylococcus aureus]] |
| - | [[Category: Dna complex]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Inhibitor]] | + | [[Category: Bax BD]] |
| - | [[Category: Isomerase]]
| + | |
| Structural highlights
Function
GYRB_STAAU 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.[HAMAP-Rule:MF_01898]
Publication Abstract from PubMed
A series of DNA gyrase inhibitors were designed based on the X-ray structure of a parent thiophene scaffold with the objective to improve biochemical and whole-cell antibacterial activity, while reducing cardiac ion channel activity. The binding mode and overall design hypothesis of one series was confirmed with a co-crystal structure with DNA gyrase. Although some analogs retained both biochemical activity and whole-cell antibacterial activity, we were unable to significantly improve the activity of the series and analogs retained activity against the cardiac ion channels, therefore we stopped optimization efforts.
Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.,Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA Bioorg Med Chem Lett. 2019 Mar 22. pii: S0960-894X(19)30168-4. doi:, 10.1016/j.bmcl.2019.03.029. PMID:30962087[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA. Structure-guided design of antibacterials that allosterically inhibit DNA gyrase. Bioorg Med Chem Lett. 2019 Mar 22. pii: S0960-894X(19)30168-4. doi:, 10.1016/j.bmcl.2019.03.029. PMID:30962087 doi:http://dx.doi.org/10.1016/j.bmcl.2019.03.029
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