2zjt - Revision history

OCA at 13:57, 13 March 2024

OCA — Wed, 13 Mar 2024 13:57:48 GMT

←Older revision		Revision as of 13:57, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2zjt' size='340' side='right'caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2zjt' size='340' side='right'caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1ab4\|1ab4]], [[1ei1\|1ei1]], [[1bjt\|1bjt]], [[1bgw\|1bgw]], [[2rgr\|2rgr]], [[2nov\|2nov]], [[1suu\|1suu]]</div></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]] 2.8Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">gyrB ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [https://pdbe.org/2zjt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [https://www.ebi.ac.uk/pdbsum/2zjt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zjt 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=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [https://pdbe.org/2zjt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [https://www.ebi.ac.uk/pdbsum/2zjt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zjt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU]] 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 (By similarity).	+	[https://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zjt ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zjt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DNA gyrase is an indispensible marvelous molecular machine in manipulating the DNA topology for the prokaryotes. In the 'two-gate' mechanism of DNA topoisomerase, T-segment navigation from N- to DNA-gate is a critical step, but the structural basis supporting this scheme is unclear. The crystal structure of DNA gyrase B' subfragment from Mycobacterium tuberculosis reveals an intrinsic homodimer. The two subunits, each consisting of a Tail and a Toprim domain, are tightly packed one another to form a 'crab-like' organization never observed previously from yeast topo II. Structural comparisons show two orientational alterations of the Tail domain, which may be dominated by a 43-residue peptide at the B' module C-terminus. A highly conserved pentapeptide mediates large-scale intrasubunit conformational change as a hinge point. Mutational studies highlight the significant roles of a negatively charge cluster on a groove at dimer interface. On the basis of structural analysis and mutation experiments, a sluice-like model for T-segment transport is proposed.
-
-	Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation.,Fu G, Wu J, Liu W, Zhu D, Hu Y, Deng J, Zhang XE, Bi L, Wang DC Nucleic Acids Res. 2009 Sep;37(17):5908-16. Epub 2009 Jul 13. PMID:19596812<ref>PMID:19596812</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2zjt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]		*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fu, G S~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Hu, Y L~~]]	+	[[Category: Fu GS]]
-	[[Category: ~~Wang, D C~~]]	+	[[Category: Hu YL]]
-	[[Category: ~~Zhu, D Y~~]]	+	[[Category: Wang DC]]
-	[[Category: ~~Atp-binding]]~~	+	[[Category: Zhu DY]]
-	~~[[Category: Dna gyrase]]~~	+
-	~~[[Category: Dna topoisomerase ii]]~~	+
-	~~[[Category: G-segment]]~~	+
-	~~[[Category: Gyrb-ctd]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: T-segment]]~~	+
-	~~[[Category: Tail]]~~	+
-	~~[[Category: Toprim~~]]	+

OCA at 17:31, 15 December 2021

OCA — Wed, 15 Dec 2021 17:31:28 GMT

←Older revision		Revision as of 17:31, 15 December 2021
Line 1:		Line 1:

	==Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation==		==Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation==
-	<StructureSection load='2zjt' size='340' side='right' caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='2zjt' size='340' side='right'caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab4\|1ab4]], [[1ei1\|1ei1]], [[1bjt\|1bjt]], [[1bgw\|1bgw]], [[2rgr\|2rgr]], [[2nov\|2nov]], [[1suu\|1suu]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ab4\|1ab4]], [[1ei1\|1ei1]], [[1bjt\|1bjt]], [[1bgw\|1bgw]], [[2rgr\|2rgr]], [[2nov\|2nov]], [[1suu\|1suu]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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='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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [~~http~~://pdbe.org/2zjt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zjt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zjt 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=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [https://pdbe.org/2zjt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [https://www.ebi.ac.uk/pdbsum/2zjt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zjt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU]] 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 (By similarity).	+	[[https://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Gyrase\|Gyrase]]	+	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fu, G S]]		[[Category: Fu, G S]]
	[[Category: Hu, Y L]]		[[Category: Hu, Y L]]

OCA at 07:06, 18 October 2018

OCA — Thu, 18 Oct 2018 07:06:41 GMT

←Older revision		Revision as of 07:06, 18 October 2018
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zj/2zjt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zj/2zjt_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:39, 5 August 2016

OCA — Fri, 05 Aug 2016 09:39:12 GMT

←Older revision		Revision as of 09:39, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation==		==Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation==
	<StructureSection load='2zjt' size='340' side='right' caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2zjt' size='340' side='right' caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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='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=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [http://www.ebi.ac.uk/pdbsum/2zjt PDBsum]</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=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [http://pdbe.org/2zjt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [http://www.ebi.ac.uk/pdbsum/2zjt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zjt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zjt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2zjt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 17:44, 25 December 2014

OCA — Thu, 25 Dec 2014 17:44:00 GMT

←Older revision		Revision as of 17:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab4\|1ab4]], [[1ei1\|1ei1]], [[1bjt\|1bjt]], [[1bgw\|1bgw]], [[2rgr\|2rgr]], [[2nov\|2nov]], [[1suu\|1suu]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab4\|1ab4]], [[1ei1\|1ei1]], [[1bjt\|1bjt]], [[1bgw\|1bgw]], [[2rgr\|2rgr]], [[2nov\|2nov]], [[1suu\|1suu]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [http://www.ebi.ac.uk/pdbsum/2zjt PDBsum]</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=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [http://www.ebi.ac.uk/pdbsum/2zjt PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fu, G S.]]	+	[[Category: Fu, G S]]
-	[[Category: Hu, Y L.]]	+	[[Category: Hu, Y L]]
-	[[Category: Wang, D C.]]	+	[[Category: Wang, D C]]
-	[[Category: Zhu, D Y.]]	+	[[Category: Zhu, D Y]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Dna gyrase]]		[[Category: Dna gyrase]]

OCA at 05:22, 3 October 2014

OCA — Fri, 03 Oct 2014 05:22:15 GMT

←Older revision		Revision as of 05:22, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2zjt\| PDB=2zjt \| SCENE= }}~~	+	==Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation==
-	===Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation===	+	<StructureSection load='2zjt' size='340' side='right' caption='[[2zjt]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19596812}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zjt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZJT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab4\|1ab4]], [[1ei1\|1ei1]], [[1bjt\|1bjt]], [[1bgw\|1bgw]], [[2rgr\|2rgr]], [[2nov\|2nov]], [[1suu\|1suu]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zjt RCSB], [http://www.ebi.ac.uk/pdbsum/2zjt PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zj/2zjt_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA gyrase is an indispensible marvelous molecular machine in manipulating the DNA topology for the prokaryotes. In the 'two-gate' mechanism of DNA topoisomerase, T-segment navigation from N- to DNA-gate is a critical step, but the structural basis supporting this scheme is unclear. The crystal structure of DNA gyrase B' subfragment from Mycobacterium tuberculosis reveals an intrinsic homodimer. The two subunits, each consisting of a Tail and a Toprim domain, are tightly packed one another to form a 'crab-like' organization never observed previously from yeast topo II. Structural comparisons show two orientational alterations of the Tail domain, which may be dominated by a 43-residue peptide at the B' module C-terminus. A highly conserved pentapeptide mediates large-scale intrasubunit conformational change as a hinge point. Mutational studies highlight the significant roles of a negatively charge cluster on a groove at dimer interface. On the basis of structural analysis and mutation experiments, a sluice-like model for T-segment transport is proposed.

-	~~==Function==~~	+	Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation.,Fu G, Wu J, Liu W, Zhu D, Hu Y, Deng J, Zhang XE, Bi L, Wang DC Nucleic Acids Res. 2009 Sep;37(17):5908-16. Epub 2009 Jul 13. PMID:19596812<ref>PMID:19596812</ref>
-	~~[[http://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU]]~~ 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~~ (~~By similarity~~).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2zjt]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Gyrase\|Gyrase]]		*[[Gyrase\|Gyrase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019596812</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Fu, G S.]]		[[Category: Fu, G S.]]
	[[Category: Hu, Y L.]]		[[Category: Hu, Y L.]]

OCA at 04:25, 13 February 2014

OCA — Thu, 13 Feb 2014 04:25:12 GMT

←Older revision		Revision as of 04:25, 13 February 2014
Line 1:		Line 1:
-	[[Image:2zjt.png\|left\|200px]]
-
	{{STRUCTURE_2zjt\| PDB=2zjt \| SCENE= }}		{{STRUCTURE_2zjt\| PDB=2zjt \| SCENE= }}
-
	===Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation===		===Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation===
		+	{{ABSTRACT_PUBMED_19596812}}

-	~~{{ABSTRACT_PUBMED_19596812}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU]] 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 (By similarity).

	==About this Structure==		==About this Structure==
-	[[2zjt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA].	+	[[2zjt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA].

	==See Also==		==See Also==
Line 14:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019596812</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019596812</ref><references group="xtra"/><references/>
-	~~[[Category: Mycobacterium tuberculosis]]~~	+
	[[Category: Fu, G S.]]		[[Category: Fu, G S.]]
	[[Category: Hu, Y L.]]		[[Category: Hu, Y L.]]

OCA at 19:35, 20 October 2012

OCA — Sat, 20 Oct 2012 19:35:37 GMT

←Older revision		Revision as of 19:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zjt]] is a 2 chain structure ~~of [[Gyrase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA].	+	[[2zjt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJT OCA].

	==See Also==		==See Also==

OCA at 07:51, 27 July 2012

OCA — Fri, 27 Jul 2012 07:51:36 GMT

←Older revision		Revision as of 07:51, 27 July 2012
Line 1:		Line 1:
	[[Image:2zjt.png\|left\|200px]]		[[Image:2zjt.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zjt", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2zjt\| PDB=2zjt \| SCENE= }}		{{STRUCTURE_2zjt\| PDB=2zjt \| SCENE= }}

	===Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation===		===Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19596812}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19596812 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19596812}}		{{ABSTRACT_PUBMED_19596812}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Gyrase]]	+	*[[Gyrase\|Gyrase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19596812~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019596812</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Fu, G S.]]		[[Category: Fu, G S.]]
Line 36:		Line 25:
	[[Category: G-segment]]		[[Category: G-segment]]
	[[Category: Gyrb-ctd]]		[[Category: Gyrb-ctd]]
		+	[[Category: Isomerase]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: T-segment]]		[[Category: T-segment]]
	[[Category: Tail]]		[[Category: Tail]]
	[[Category: Toprim]]		[[Category: Toprim]]

OCA: Protected "2zjt" [edit=sysop:move=sysop]

OCA — Mon, 27 Dec 2010 01:17:52 GMT

Protected "2zjt" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:17, 27 December 2010