6y8n - Revision history

OCA at 13:21, 24 January 2024

OCA — Wed, 24 Jan 2024 13:21:51 GMT

←Older revision		Revision as of 13:21, 24 January 2024
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	<StructureSection load='6y8n' size='340' side='right'caption='[[6y8n]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='6y8n' size='340' side='right'caption='[[6y8n]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y8n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_19527 Atcc 19527~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y8n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_thermoresistibile Mycolicibacterium thermoresistibile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y8N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OGH:4-[(1~{S},5~{R})-6-azanyl-3-azabicyclo[3.1.0]hexan-3-yl]-6-fluoranyl-~{N}-methyl-2-(2-methylpyrimidin-5-yl)oxy-9~{H}-pyrimido[4,5-b]indol-8-amine'>OGH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6y8l\|6y8l]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OGH:4-[(1~{S},5~{R})-6-azanyl-3-azabicyclo[3.1.0]hexan-3-yl]-6-fluoranyl-~{N}-methyl-2-(2-methylpyrimidin-5-yl)oxy-9~{H}-pyrimido[4,5-b]indol-8-amine'>OGH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB, RMCT_1109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1797 ATCC 19527])</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=6y8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8n OCA], [https://pdbe.org/6y8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8n RCSB], [https://www.ebi.ac.uk/pdbsum/6y8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8n ProSAT]</span></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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.6.2.2 5.6.2.2] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6y8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8n OCA], [~~http~~://pdbe.org/6y8n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y8n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y8n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A117ILT2_MYCTH A0A117ILT2_MYCTH]~~] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01898]	+	[https://www.uniprot.org/uniprot/G7CIP8_MYCT3 G7CIP8_MYCT3] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[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 6y8n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6y8n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 19527]]
-	[[Category: DNA topoisomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Charrier, C]]	+	[[Category: Mycolicibacterium thermoresistibile]]
-	[[Category: Cooper~~, I R~~]]	+	[[Category: Charrier C]]
-	[[Category: Henderson~~, S R~~]]	+	[[Category: Cooper IR]]
-	[[Category: Lawson~~, D M~~]]	+	[[Category: Henderson SR]]
-	[[Category: Malone, B]]	+	[[Category: Lawson DM]]
-	[[Category: Maxwell, A]]	+	[[Category: Malone B]]
-	[[Category: McGarry~~, D H~~]]	+	[[Category: Maxwell A]]
-	[[Category: Mitchenall~~, L A~~]]	+	[[Category: McGarry DH]]
-	[[Category: Pichowicz, M]]	+	[[Category: Mitchenall LA]]
-	[[Category: Salisbury, A]]	+	[[Category: Pichowicz M]]
-	[[Category: Stevenson~~, C E.M~~]]	+	[[Category: Salisbury A]]
-	[[Category: Zholnerovych, Y]]	+	[[Category: Stevenson CEM]]
-	~~[[Category: Binding site]]~~	+	[[Category: Zholnerovych Y]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna gyrase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Redx03863 iv~~]]	+

OCA at 07:48, 30 September 2020

OCA — Wed, 30 Sep 2020 07:48:59 GMT

←Older revision		Revision as of 07:48, 30 September 2020
Line 1:		Line 1:

	==Mycobacterium thermoresistibile GyrB21 in complex with Redx03863==		==Mycobacterium thermoresistibile GyrB21 in complex with Redx03863==
-	<StructureSection load='6y8n' size='340' side='right'caption='[[6y8n]]' scene=''>	+	<StructureSection load='6y8n' size='340' side='right'caption='[[6y8n]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y8n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19527 Atcc 19527]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y8N FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8n OCA], [http://pdbe.org/6y8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y8n RCSB], [http://www.ebi.ac.uk/pdbsum/6y8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8n ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OGH:4-[(1~{S},5~{R})-6-azanyl-3-azabicyclo[3.1.0]hexan-3-yl]-6-fluoranyl-~{N}-methyl-2-(2-methylpyrimidin-5-yl)oxy-9~{H}-pyrimido[4,5-b]indol-8-amine'>OGH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6y8l\|6y8l]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB, RMCT_1109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1797 ATCC 19527])</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 DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.6.2.2 5.6.2.2] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8n OCA], [http://pdbe.org/6y8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y8n RCSB], [http://www.ebi.ac.uk/pdbsum/6y8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8n ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A117ILT2_MYCTH A0A117ILT2_MYCTH]] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01898]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OBJECTIVES: To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches. METHODS: Redx03863 and Redx04739 were tested in antibacterial assays, and also against their target, DNA gyrase, using DNA supercoiling and ATPase assays. X-ray crystallography was used to determine the structure of the gyrase B protein ATPase sub-domain from Mycobacterium smegmatis complexed with the aminocoumarin drug novobiocin, and structures of the same domain from Mycobacterium thermoresistibile complexed with novobiocin, and also with Redx03863. RESULTS: Both compounds, Redx03863 and Redx04739, were active against selected Gram-positive and Gram-negative species, with Redx03863 being the more potent, and Redx04739 showing selectivity against M. smegmatis. Both compounds were potent inhibitors of the supercoiling and ATPase reactions of DNA gyrase, but did not appreciably affect the ATP-independent relaxation reaction. The structure of Redx03863 bound to the gyrase B protein ATPase sub-domain from M. thermoresistibile shows that it binds at a site adjacent to the ATP- and novobiocin-binding sites. We found that most of the mutations that we made in the Redx03863-binding pocket, based on the structure, rendered gyrase inactive. CONCLUSIONS: Redx03863 and Redx04739 inhibit gyrase by preventing the binding of ATP. The fact that the Redx03863-binding pocket is distinct from that of novobiocin, coupled with the lack of activity of resistant mutants, suggests that such compounds could have potential to be further exploited as antibiotics.
		+
		+	Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase.,Henderson SR, Stevenson CEM, Malone B, Zholnerovych Y, Mitchenall LA, Pichowicz M, McGarry DH, Cooper IR, Charrier C, Salisbury AM, Lawson DM, Maxwell A J Antimicrob Chemother. 2020 Jul 30. pii: 5878045. doi: 10.1093/jac/dkaa286. PMID:32728686<ref>PMID:32728686</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y8n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 19527]]
		+	[[Category: DNA topoisomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Charrier C]]	+	[[Category: Charrier, C]]
-	[[Category: Cooper IR]]	+	[[Category: Cooper, I R]]
-	[[Category: Henderson SR]]	+	[[Category: Henderson, S R]]
-	[[Category: Lawson DM]]	+	[[Category: Lawson, D M]]
-	[[Category: Malone B]]	+	[[Category: Malone, B]]
-	[[Category: Maxwell A]]	+	[[Category: Maxwell, A]]
-	[[Category: McGarry DH]]	+	[[Category: McGarry, D H]]
-	[[Category: Mitchenall LA]]	+	[[Category: Mitchenall, L A]]
-	[[Category: Pichowicz M]]	+	[[Category: Pichowicz, M]]
-	[[Category: Salisbury A]]	+	[[Category: Salisbury, A]]
-	[[Category: Stevenson ~~CEM~~]]	+	[[Category: Stevenson, C E.M]]
-	[[Category: Zholnerovych Y]]	+	[[Category: Zholnerovych, Y]]
		+	[[Category: Binding site]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna gyrase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Isomerase]]
		+	[[Category: Redx03863 iv]]

OCA at 09:49, 12 August 2020

OCA — Wed, 12 Aug 2020 09:49:21 GMT

←Older revision		Revision as of 09:49, 12 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6y8n is ~~ON HOLD until Paper Publication~~	+	==Mycobacterium thermoresistibile GyrB21 in complex with Redx03863==
-		+	<StructureSection load='6y8n' size='340' side='right'caption='[[6y8n]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y8N FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8n OCA], [http://pdbe.org/6y8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y8n RCSB], [http://www.ebi.ac.uk/pdbsum/6y8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8n ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Charrier C]]
		+	[[Category: Cooper IR]]
		+	[[Category: Henderson SR]]
		+	[[Category: Lawson DM]]
		+	[[Category: Malone B]]
		+	[[Category: Maxwell A]]
		+	[[Category: McGarry DH]]
		+	[[Category: Mitchenall LA]]
		+	[[Category: Pichowicz M]]
		+	[[Category: Salisbury A]]
		+	[[Category: Stevenson CEM]]
		+	[[Category: Zholnerovych Y]]

OCA at 08:37, 18 March 2020

OCA — Wed, 18 Mar 2020 08:37:50 GMT

←Older revision		Revision as of 08:37, 18 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y8n is ON HOLD	+	The entry 6y8n is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6y8n" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:18:09 GMT

Protected "6y8n" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y8n is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Mar 2020 06:18:08 GMT

New page: '''Unreleased structure''' The entry 6y8n is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y8n is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]