7z9g - Revision history

OCA at 06:19, 19 July 2023

OCA — Wed, 19 Jul 2023 06:19:20 GMT

←Older revision		Revision as of 06:19, 19 July 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7z9g]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655] and [https://en.wikipedia.org/wiki/Escherichia_phage_Mu Escherichia phage Mu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9G FirstGlance]. <br>		<table><tr><td colspan='2'>[[7z9g]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655] and [https://en.wikipedia.org/wiki/Escherichia_phage_Mu Escherichia phage Mu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IM0:4-[[3-(2-azanylethoxy)-2-oxidanyl-4-[[5-[[(2~{S})-2-[[4-[(6-oxidanylnaphthalen-2-yl)carbonylamino]phenyl]carbonylamino]-3-(1~{H}-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic+acid'>IM0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.25Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IM0:4-[[3-(2-azanylethoxy)-2-oxidanyl-4-[[5-[[(2~{S})-2-[[4-[(6-oxidanylnaphthalen-2-yl)carbonylamino]phenyl]carbonylamino]-3-(1~{H}-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic+acid'>IM0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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=7z9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9g OCA], [https://pdbe.org/7z9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9g RCSB], [https://www.ebi.ac.uk/pdbsum/7z9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9g ProSAT]</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=7z9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9g OCA], [https://pdbe.org/7z9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9g RCSB], [https://www.ebi.ac.uk/pdbsum/7z9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9g ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7z9g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7z9g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:25, 15 February 2023

OCA — Wed, 15 Feb 2023 10:25:13 GMT

←Older revision		Revision as of 10:25, 15 February 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7z9g is ~~ON HOLD until Paper~~ Publication	+	==E.coli gyrase holocomplex with 217 bp DNA and Albi-2==
		+	<StructureSection load='7z9g' size='340' side='right'caption='[[7z9g]], [[Resolution\|resolution]] 3.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7z9g]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655] and [https://en.wikipedia.org/wiki/Escherichia_phage_Mu Escherichia phage Mu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z9G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IM0:4-[[3-(2-azanylethoxy)-2-oxidanyl-4-[[5-[[(2~{S})-2-[[4-[(6-oxidanylnaphthalen-2-yl)carbonylamino]phenyl]carbonylamino]-3-(1~{H}-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic+acid'>IM0</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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=7z9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z9g OCA], [https://pdbe.org/7z9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z9g RCSB], [https://www.ebi.ac.uk/pdbsum/7z9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z9g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GYRA_ECOLI GYRA_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:12051842</ref> <ref>PMID:18642932</ref> <ref>PMID:19965760</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 A resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.

-	~~Authors~~:	+	Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.,Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D Nat Catal. 2023;6(1):52-67. doi: 10.1038/s41929-022-00904-1. Epub 2023 Jan 23. PMID:36741192<ref>PMID:36741192</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7z9g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli str. K-12 substr. MG1655]]
		+	[[Category: Escherichia phage Mu]]
		+	[[Category: Large Structures]]
		+	[[Category: Ghilarov D]]
		+	[[Category: Heddle JGH]]

OCA at 04:29, 28 September 2022

OCA — Wed, 28 Sep 2022 04:29:37 GMT

←Older revision		Revision as of 04:29, 28 September 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7z9g is ON HOLD	+	The entry 7z9g is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 03:41, 25 August 2022

OCA — Thu, 25 Aug 2022 03:41:02 GMT

←Older revision		Revision as of 03:41, 25 August 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7z9g is ON HOLD ~~until Paper Publication~~	+	The entry 7z9g is ON HOLD

	Authors:		Authors:

OCA at 11:44, 4 May 2022

OCA — Wed, 04 May 2022 11:44:12 GMT

←Older revision		Revision as of 11:44, 4 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7z9g is ON HOLD	+	The entry 7z9g is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7z9g" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2022 09:48:48 GMT

Protected "7z9g" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:48, 30 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z9g is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Mar 2022 09:48:47 GMT

New page: '''Unreleased structure''' The entry 7z9g is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7z9g is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]