1zi0: Difference between revisions

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-[[Image:1zi0.gif|left|200px]]
- {{Structure
+==A Superhelical Spiral in Escherichia coli DNA Gyrase A C-terminal Domain Imparts Unidirectional Supercoiling Bias==
-|PDB= 1zi0 |SIZE=350|CAPTION= <scene name='initialview01'>1zi0</scene>, resolution 2.60&Aring;
+<StructureSection load='1zi0' size='340' side='right'caption='[[1zi0]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[1zi0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZI0 FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-|GENE= gyrA, hisW, nalA, parD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zi0 OCA], [https://pdbe.org/1zi0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zi0 RCSB], [https://www.ebi.ac.uk/pdbsum/1zi0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zi0 ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zi0 OCA], [http://www.ebi.ac.uk/pdbsum/1zi0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zi0 RCSB]</span>
+[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>
-}}
+== 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/zi/1zi0_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/main_output.php?pdb_ID=1zi0 ConSurf].
+<div style="clear:both"></div>
-'''A Superhelical Spiral in Escherichia coli DNA Gyrase A C-terminal Domain Imparts Unidirectional Supercoiling Bias'''
+==See Also==
+*[[Gyrase 3D Structures|Gyrase 3D Structures]]
+== References ==
-==Overview==
+<references/>
-DNA gyrase is unique among type II topoisomerases in that its DNA supercoiling activity is unidirectional. The C-terminal domain of the gyrase A subunit (GyrA-CTD) is required for this supercoiling bias. We report here the x-ray structure of the Escherichia coli GyrA-CTD (Protein Data Bank code 1ZI0). The E. coli GyrA-CTD adopts a circular-shaped beta-pinwheel fold first seen in the Borrelia burgdorferi GyrA-CTD. However, whereas the B. burgdorferi GyrA-CTD is flat, the E. coli GyrA-CTD is spiral. DNA relaxation assays reveal that the E. coli GyrA-CTD wraps DNA inducing substantial (+) superhelicity, while the B. burgdorferi GyrA-CTD introduces a more modest (+) superhelicity. The observation of a superhelical spiral in the present structure and that of the Bacillus stearothermophilus ParC-CTD structure suggests unexpected similarities in substrate selectivity between gyrase and Topo IV enzymes. We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling.
+__TOC__
+</StructureSection>
-==About this Structure==
-ZI0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZI0 OCA].
-==Reference==
-A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias., Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL, J Biol Chem. 2005 Jul 15;280(28):26177-84. Epub 2005 May 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15897198 15897198]
-[[Category: DNA topoisomerase (ATP-hydrolyzing)]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Graybosch, D M.]]
+[[Category: Graybosch DM]]
-[[Category: Huetsch, J C.]]
+[[Category: Huetsch JC]]
-[[Category: Ruthenburg, A J.]]
+[[Category: Ruthenburg AJ]]
-[[Category: Verdine, G L.]]
+[[Category: Verdine GL]]
-[[Category: beta pinwheel]]
-[[Category: dna wrapping]]
-[[Category: gyrase]]
-[[Category: spiralling beta pinwheel]]
-[[Category: topoisomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:36:53 2008''