2gyk: Difference between revisions

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 ==Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)==
-<StructureSection load='2gyk' size='340' side='right' caption='[[2gyk]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='2gyk' size='340' side='right'caption='[[2gyk]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gyk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GYK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gyk]] is a 4 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=2GYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GYK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1emv|1emv]], [[1bxi|1bxi]], [[2gze|2gze]], [[2gzf|2gzf]], [[2gzg|2gzg]], [[2gzi|2gzi]], [[2gzj|2gzj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IMM9_ECOLI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), col, cei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gyk OCA], [https://pdbe.org/2gyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gyk RCSB], [https://www.ebi.ac.uk/pdbsum/2gyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gyk ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] </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=2gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gyk OCA], [http://pdbe.org/2gyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gyk RCSB], [http://www.ebi.ac.uk/pdbsum/2gyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gyk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX]] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity. [[http://www.uniprot.org/uniprot/CEA9_ECOLX CEA9_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity.  Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
+[https://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity.
 == 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/gy/2gyk_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/2gyk_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 22: / Line 20: @@
 </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=2gyk ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of the cytotoxic endonuclease domain from the bacterial toxin colicin E9 in complex with its cognate immunity protein Im9 reveals that the inhibitor does not bind at the active site, the core of which comprises the HNH motif found in intron-encoded homing endonucleases, but rather at an adjacent position leaving the active site exposed yet unable to bind DNA because of steric and electrostatic clashes with incoming substrate. Although its mode of action is unorthodox, Im9 is a remarkably effective inhibitor since it folds within milliseconds and then associates with its target endonuclease at the rate of diffusion to form an inactive complex with sub-femtomolar binding affinity. This hyperefficient mechanism of inhibition could be well suited to other toxic enzyme systems, particularly where the substrate is a polymer extending beyond the boundaries of the active site.
-Structural and mechanistic basis of immunity toward endonuclease colicins.,Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM Nat Struct Biol. 1999 Mar;6(3):243-52. PMID:10074943<ref>PMID:10074943</ref>
+==See Also==
+*[[Colicin 3D structures|Colicin 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
-</div>
-<div class="pdbe-citations 2gyk" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Deoxyribonuclease I]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ecoli]]
+[[Category: Large Structures]]
-[[Category: Hemmings, A M]]
+[[Category: Hemmings AM]]
-[[Category: Kolade, O O]]
+[[Category: Kolade OO]]
-[[Category: Kuhlmann, U C]]
+[[Category: Kuhlmann UC]]
-[[Category: Santi, P S]]
+[[Category: Santi PS]]
-[[Category: 4-helix bundle]]
-[[Category: Antibiotic-antibiotic inhibitor complex]]
-[[Category: Dnase domain]]
-[[Category: Hnh-motif]]
-[[Category: Protein-protein complex]]