1cy9: Difference between revisions

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[[Image:1cy9.gif|left|200px]]


{{Structure
==CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM==
|PDB= 1cy9 |SIZE=350|CAPTION= <scene name='initialview01'>1cy9</scene>, resolution 1.80&Aring;
<StructureSection load='1cy9' size='340' side='right'caption='[[1cy9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1cy9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CY9 FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cy9 OCA], [https://pdbe.org/1cy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cy9 RCSB], [https://www.ebi.ac.uk/pdbsum/1cy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cy9 ProSAT]</span></td></tr>
}}
</table>
== Function ==
[https://www.uniprot.org/uniprot/TOP1_ECOLI TOP1_ECOLI] Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.<ref>PMID:9497321</ref> <ref>PMID:10681504</ref> <ref>PMID:21482796</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/cy/1cy9_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=1cy9 ConSurf].
<div style="clear:both"></div>


'''CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM'''
==See Also==
 
*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 
== References ==
==Overview==
<references/>
DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodiester backbone. It has been proposed that both type IA and type II enzymes change conformation dramatically during the reaction cycle in order to accomplish these transformations. In the case of Escherichia coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The fragment is composed of two domains, and while the domains themselves remain largely unchanged, their relative arrangement can change dramatically.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Escherichia coli K-12]]
1CY9 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=1CY9 OCA].
[[Category: Large Structures]]
 
[[Category: Feinberg H]]
==Reference==
[[Category: Lima C]]
Conformational changes in E. coli DNA topoisomerase I., Feinberg H, Lima CD, Mondragon A, Nat Struct Biol. 1999 Oct;6(10):918-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10504724 10504724]
[[Category: Mondragon A]]
[[Category: DNA topoisomerase]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Feinberg, H.]]
[[Category: Lima, C.]]
[[Category: Mondragon, A.]]
[[Category: decatenating enzyme]]
[[Category: dna topoisomerase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:30:22 2008''
Retrieved from "https://proteopedia.org/1cy9"