1ecl: Difference between revisions

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OCA

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-[[Image:1ecl.gif|left|200px]]<br /><applet load="1ecl" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ecl, resolution 1.9&Aring;" />
-'''AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1).'''<br />
-==Overview==
+==AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1).==
-The three-dimensional structure of the 67K amino-terminal fragment of, Escherichia coli DNA topoisomerase I has been determined to 2.2 A, resolution. The polypeptide folds in an unusual way to give four distinct, domains enclosing a hole large enough to accommodate a double-stranded, DNA. The active-site tyrosyl residue, which is involved in the transient, breakage of a DNA strand and the formation of a covalent enzyme-DNA, intermediate, is present at the interface of two domains. The structure, suggests a plausible mechanism by which E. coli DNA topoisomerase I and, other members of the same DNA topoisomerase subfamily could catalyse the, passage of one DNA strand through a transient break in another strand.
+<StructureSection load='1ecl' size='340' side='right'caption='[[1ecl]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ecl]] is a 1 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=1ECL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ECL FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=1ecl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ecl OCA], [https://pdbe.org/1ecl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ecl RCSB], [https://www.ebi.ac.uk/pdbsum/1ecl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ecl 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/ec/1ecl_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=1ecl ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-ECL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ECL OCA].
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I., Lima CD, Wang JC, Mondragon A, Nature. 1994 Jan 13;367(6459):138-46. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8114910 8114910]
+__TOC__
-[[Category: DNA topoisomerase]]
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Lima, C.D.]]
+[[Category: Lima CD]]
-[[Category: Mondragon, A.]]
+[[Category: Mondragon A]]
-[[Category: Wang, J.C.]]
+[[Category: Wang JC]]
-[[Category: bacterial type i]]
-[[Category: dna cleavage]]
-[[Category: strand passage]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:53:50 2007''