6zt3 - Revision history

OCA at 11:57, 1 February 2024

OCA — Thu, 01 Feb 2024 11:57:56 GMT

←Older revision		Revision as of 11:57, 1 February 2024
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	<StructureSection load='6zt3' size='340' side='right'caption='[[6zt3]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='6zt3' size='340' side='right'caption='[[6zt3]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zt3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Mycs2 Mycs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zt3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZT3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.56Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB, MSMEG_0005, MSMEI_0007 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [https://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=6zt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zt3 OCA], [https://pdbe.org/6zt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zt3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zt3 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=6zt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zt3 OCA], [https://pdbe.org/6zt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zt3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zt3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GYRB_MYCS2 GYRB_MYCS2]] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:8878580) 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]<ref>PMID:8878580</ref>	+	[https://www.uniprot.org/uniprot/GYRB_MYCS2 GYRB_MYCS2] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:8878580) 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]<ref>PMID:8878580</ref>
	<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 6zt3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6zt3" 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: ~~Mycs2~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: Feng, L]]	+	[[Category: Feng L]]
-	[[Category: Lawson~~, D M~~]]	+	[[Category: Lawson DM]]
-	[[Category: Maxwell, A]]	+	[[Category: Maxwell A]]
-	[[Category: Mi, K]]	+	[[Category: Mi K]]
-	[[Category: Mitchenall~~, L A~~]]	+	[[Category: Mitchenall LA]]
-	[[Category: Mundy~~, J E.A~~]]	+	[[Category: Mundy JEA]]
-	[[Category: Stevenson~~, C E.M]]~~	+	[[Category: Stevenson CEM]]
-	~~[[Category: Atpase domain]]~~	+
-	~~[[Category: Ghkl superfamily]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Type iia topoisomerase~~]]	+

OCA at 08:30, 21 April 2021

OCA — Wed, 21 Apr 2021 08:30:12 GMT

←Older revision		Revision as of 08:30, 21 April 2021
Line 1:		Line 1:

	==N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP==		==N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP==
-	<StructureSection load='6zt3' size='340' side='right'caption='[[6zt3]]' scene=''>	+	<StructureSection load='6zt3' size='340' side='right'caption='[[6zt3]], [[Resolution\|resolution]] 1.56Å' 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=6ZT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zt3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZT3 FirstGlance]. <br>
-	</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=6zt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zt3 OCA], [https://pdbe.org/6zt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zt3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zt3 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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB, MSMEG_0005, MSMEI_0007 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [https://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=6zt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zt3 OCA], [https://pdbe.org/6zt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zt3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zt3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/GYRB_MYCS2 GYRB_MYCS2]] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:8878580) 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]<ref>PMID:8878580</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA gyrase, a type II topoisomerase, introduces negative supercoils into DNA using ATP hydrolysis. The highly effective gyrase-targeted drugs, fluoroquinolones (FQs), interrupt gyrase by stabilizing a DNA-cleavage complex, a transient intermediate in the supercoiling cycle, leading to double-stranded DNA breaks. MfpA, a pentapeptide-repeat protein in mycobacteria, protects gyrase from FQs, but its molecular mechanism remains unknown. Here, we show that Mycobacterium smegmatis MfpA (MsMfpA) inhibits negative supercoiling by M. smegmatis gyrase (Msgyrase) in the absence of FQs, while in their presence, MsMfpA decreases FQ-induced DNA cleavage, protecting the enzyme from these drugs. MsMfpA stimulates the ATPase activity of Msgyrase by directly interacting with the ATPase domain (MsGyrB47), which was confirmed through X-ray crystallography of the MsMfpA-MsGyrB47 complex, and mutational analysis, demonstrating that MsMfpA mimics a T (transported) DNA segment. These data reveal the molecular mechanism whereby MfpA modulates the activity of gyrase and may provide a general molecular basis for the action of other pentapeptide-repeat proteins.
		+
		+	The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic.,Feng L, Mundy JEA, Stevenson CEM, Mitchenall LA, Lawson DM, Mi K, Maxwell A Proc Natl Acad Sci U S A. 2021 Mar 16;118(11). pii: 2016705118. doi:, 10.1073/pnas.2016705118. PMID:33836580<ref>PMID:33836580</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zt3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Feng L]]	+	[[Category: Mycs2]]
-	[[Category: Lawson DM]]	+	[[Category: Feng, L]]
-	[[Category: Maxwell A]]	+	[[Category: Lawson, D M]]
-	[[Category: Mi K]]	+	[[Category: Maxwell, A]]
-	[[Category: Mitchenall LA]]	+	[[Category: Mi, K]]
-	[[Category: Mundy ~~JEA~~]]	+	[[Category: Mitchenall, L A]]
-	[[Category: Stevenson ~~CEM~~]]	+	[[Category: Mundy, J E.A]]
		+	[[Category: Stevenson, C E.M]]
		+	[[Category: Atpase domain]]
		+	[[Category: Ghkl superfamily]]
		+	[[Category: Isomerase]]
		+	[[Category: Type iia topoisomerase]]

OCA at 14:42, 3 March 2021

OCA — Wed, 03 Mar 2021 14:42:58 GMT

←Older revision		Revision as of 14:42, 3 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zt3 is ~~ON HOLD until Paper Publication~~	+	==N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP==
-		+	<StructureSection load='6zt3' size='340' side='right'caption='[[6zt3]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZT3 FirstGlance]. <br>
-	~~Description~~:	+	</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=6zt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zt3 OCA], [https://pdbe.org/6zt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zt3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zt3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Feng L]]
		+	[[Category: Lawson DM]]
		+	[[Category: Maxwell A]]
		+	[[Category: Mi K]]
		+	[[Category: Mitchenall LA]]
		+	[[Category: Mundy JEA]]
		+	[[Category: Stevenson CEM]]

OCA: Protected "6zt3" [edit=sysop:move=sysop]

OCA — Wed, 29 Jul 2020 09:33:03 GMT

Protected "6zt3" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:33, 29 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zt3 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 29 Jul 2020 09:33:02 GMT

New page: '''Unreleased structure''' The entry 6zt3 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6zt3 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]