7dpr: Difference between revisions
New page: '''Unreleased structure''' The entry 7dpr is ON HOLD until Paper Publication Authors: Yu, Y., Zhou, H. Description: E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzo... |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzoate== | |||
<StructureSection load='7dpr' size='340' side='right'caption='[[7dpr]], [[Resolution|resolution]] 1.75Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7dpr]] 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=7DPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DPR FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AX7:1H-BENZIMIDAZOL-2-AMINE'>AX7</scene>, <scene name='pdbligand=HE9:methyl+3,4-bis(oxidanyl)benzoate'>HE9</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=7dpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dpr OCA], [https://pdbe.org/7dpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dpr RCSB], [https://www.ebi.ac.uk/pdbsum/7dpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dpr ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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;"> | |||
== Publication Abstract from PubMed == | |||
DNA gyrase is an essential DNA topoisomerase that exists only in bacteria. Since novobiocin was withdrawn from the market, new scaffolds and new mechanistic GyrB inhibitors are urgently needed. In this study, we employed fragment screening and X-ray crystallography to identify new building blocks, as well as their binding mechanisms, to support the discovery of new GyrB inhibitors. In total, 84 of the 618 chemical fragments were shown to either thermally stabilize the ATPase domain of Escherichia coli GyrB or inhibit the ATPase activity of E. coli gyrase. Among them, the IC50 values of fragments 10 and 23 were determined to be 605.3 muM and 446.2 muM, respectively. Cocrystal structures of the GyrB ATPase domain with twelve fragment hits were successfully determined at a high resolution. All twelve fragments were deeply inserted in the pocket and formed H-bonds with Asp73 and Thr165, and six fragments formed an additional H-bond with the backbone oxygen of Val71. Fragment screening further highlighted the capability of Asp73, Thr165 and Val71 to bind chemicals and provided diverse building blocks for the design of GyrB inhibitors. | |||
Identification of new building blocks by fragment screening for discovering GyrB inhibitors.,Yu Y, Guo J, Cai Z, Ju Y, Xu J, Gu Q, Zhou H Bioorg Chem. 2021 Sep;114:105040. doi: 10.1016/j.bioorg.2021.105040. Epub 2021, May 31. PMID:34098257<ref>PMID:34098257</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7dpr" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
==See Also== | |||
*[[Gyrase 3D Structures|Gyrase 3D Structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli K-12]] | |||
[[Category: Large Structures]] | |||
[[Category: Yu Y]] | |||
[[Category: Zhou H]] | |||
Latest revision as of 19:37, 29 November 2023
E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzoateE. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzoate
Structural highlights
FunctionGYRB_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 PubMedDNA gyrase is an essential DNA topoisomerase that exists only in bacteria. Since novobiocin was withdrawn from the market, new scaffolds and new mechanistic GyrB inhibitors are urgently needed. In this study, we employed fragment screening and X-ray crystallography to identify new building blocks, as well as their binding mechanisms, to support the discovery of new GyrB inhibitors. In total, 84 of the 618 chemical fragments were shown to either thermally stabilize the ATPase domain of Escherichia coli GyrB or inhibit the ATPase activity of E. coli gyrase. Among them, the IC50 values of fragments 10 and 23 were determined to be 605.3 muM and 446.2 muM, respectively. Cocrystal structures of the GyrB ATPase domain with twelve fragment hits were successfully determined at a high resolution. All twelve fragments were deeply inserted in the pocket and formed H-bonds with Asp73 and Thr165, and six fragments formed an additional H-bond with the backbone oxygen of Val71. Fragment screening further highlighted the capability of Asp73, Thr165 and Val71 to bind chemicals and provided diverse building blocks for the design of GyrB inhibitors. Identification of new building blocks by fragment screening for discovering GyrB inhibitors.,Yu Y, Guo J, Cai Z, Ju Y, Xu J, Gu Q, Zhou H Bioorg Chem. 2021 Sep;114:105040. doi: 10.1016/j.bioorg.2021.105040. Epub 2021, May 31. PMID:34098257[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||