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| | ==Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor== | | ==Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor== |
| - | <StructureSection load='4duh' size='340' side='right' caption='[[4duh]], [[Resolution|resolution]] 1.50Å' scene=''> | + | <StructureSection load='4duh' size='340' side='right'caption='[[4duh]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4duh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DUH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DUH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4duh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DUH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RLI:4-{[4-METHYL-2-(PROPANOYLAMINO)-4,5-BI-1,3-THIAZOL-2-YL]AMINO}BENZOIC+ACID'>RLI</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RLI:4-{[4-METHYL-2-(PROPANOYLAMINO)-4,5-BI-1,3-THIAZOL-2-YL]AMINO}BENZOIC+ACID'>RLI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kzn|1kzn]], [[1aj6|1aj6]]</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=4duh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4duh OCA], [https://pdbe.org/4duh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4duh RCSB], [https://www.ebi.ac.uk/pdbsum/4duh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4duh ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrB, acrB, himB, hisU, nalC, parA, pcbA, b3699, JW5625 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4duh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4duh OCA], [http://pdbe.org/4duh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4duh RCSB], [http://www.ebi.ac.uk/pdbsum/4duh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4duh ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [[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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Gyrase|Gyrase]] | + | *[[Gyrase 3D Structures|Gyrase 3D Structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Brvar, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Perdih, A]] | + | [[Category: Brvar M]] |
| - | [[Category: Renko, M]] | + | [[Category: Perdih A]] |
| - | [[Category: Solmajer, T]] | + | [[Category: Renko M]] |
| - | [[Category: Turk, D]] | + | [[Category: Solmajer T]] |
| - | [[Category: Antibacterial]]
| + | [[Category: Turk D]] |
| - | [[Category: Dna gyrase b]]
| + | |
| - | [[Category: Gyrase]]
| + | |
| - | [[Category: Isomerase-isomerase inhibitor complex]]
| + | |
| - | [[Category: Structure-based drug design]]
| + | |
| Structural highlights
Function
[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.[1] [2] [3]
Publication Abstract from PubMed
Bacterial DNA gyrase is a well-established and validated target for the development of novel antibacterials. Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4'-methyl-N(2)-phenyl-[4,5'-bithiazole]-2,2'-diamine inhibitors of gyrase B with a low micromolar inhibitory activity by implementing a two-step structure-based design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques (differential scanning fluorimetry, surface plasmon resonance, and microscale thermophoresis). The binding mode of the potent inhibitor 18 was revealed by X-ray crystallography, confirming our initial in silico binding model. Furthermore, the high resolution of the complex structure allowed for the placement of the Gly97-Ser108 flexible loop, thus revealing its role in binding of this class of compounds. The crystal structure of the complex protein G24 and inhibitor 18 provides valuable information for further optimization of this novel class of DNA gyrase B inhibitors.
Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors.,Brvar M, Perdih A, Renko M, Anderluh G, Turk D, Solmajer T J Med Chem. 2012 Jul 26;55(14):6413-26. Epub 2012 Jul 5. PMID:22731783[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Noble CG, Maxwell A. The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J Mol Biol. 2002 Apr 26;318(2):361-71. PMID:12051843 doi:http://dx.doi.org/10.1016/S0022-2836(02)00049-9
- ↑ Sissi C, Chemello A, Vazquez E, Mitchenall LA, Maxwell A, Palumbo M. DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action. Biochemistry. 2008 Aug 19;47(33):8538-45. doi: 10.1021/bi800480j. Epub 2008 Jul, 22. PMID:18642932 doi:http://dx.doi.org/10.1021/bi800480j
- ↑ Schoeffler AJ, May AP, Berger JM. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res. 2010 Jul 31. PMID:20675723 doi:10.1093/nar/gkq665
- ↑ Brvar M, Perdih A, Renko M, Anderluh G, Turk D, Solmajer T. Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. J Med Chem. 2012 Jul 26;55(14):6413-26. Epub 2012 Jul 5. PMID:22731783 doi:10.1021/jm300395d
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