2k0d: Difference between revisions

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-{{Seed}}
-[[Image:2k0d.png|left|200px]]
-<!--
+==NMR structure of a mutant colicin e7 immunity protein im7 with an extended helix III==
-The line below this paragraph, containing "STRUCTURE_2k0d", creates the "Structure Box" on the page.
+<StructureSection load='2k0d' size='340' side='right'caption='[[2k0d]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2k0d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K0D FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2k0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k0d OCA], [https://pdbe.org/2k0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k0d RCSB], [https://www.ebi.ac.uk/pdbsum/2k0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k0d ProSAT]</span></td></tr>
-{{STRUCTURE_2k0d|  PDB=2k0d  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IMM7_ECOLX IMM7_ECOLX] This protein is able to protect a cell, which harbors the plasmid ColE7 encoding colicin E7, against colicin E7, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity. Dimeric ImmE7 may possess a RNase activity that cleaves its own mRNA at a specific site and thus autoregulates translational expression of the downstream ceiE7 gene as well as degradation of the upstream ceaE7 mRNA.
+== 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/k0/2k0d_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=2k0d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The small (87-residue) alpha-helical protein Im7 (an inhibitor protein for colicin E7 that provides immunity to cells producing colicin E7) folds via a three-state mechanism involving an on-pathway intermediate. This kinetic intermediate contains three of four native helices that are oriented in a non-native manner so as to minimise exposed hydrophobic surface area at this point in folding. The short (6-residue) helix III has been shown to be unstructured in the intermediate ensemble and does not dock onto the developing hydrophobic core until after the rate-limiting transition state has been traversed. After helix III has docked, it adopts an alpha-helical secondary structure, and the side chains of residues within this region provide contacts that are crucial to native-state stability. In order to probe further the role of helix III in the folding mechanism of Im7, we created a variant that contains an eight-amino-acid polyalanine-like helix stabilised by a Glu-Arg salt bridge and an Asn-Pro-Gly capping motif, juxtaposed C-terminal to the natural 6-residue helix III. The effect of this insertion on the structure of the native protein and its folding mechanism were studied using NMR and varphi-value analysis, respectively. The results reveal a robust native structure that is not perturbed by the presence of the extended helix III. Mutational analysis performed to probe the folding mechanism of the redesigned protein revealed a conserved mechanism involving the canonical three-helical intermediate. The results suggest that folding via a three-helical species stabilised by both native and non-native interactions is an essential feature of Im7 folding, independent of the helical propensity of helix III.
-===NMR structure of a mutant colicin e7 immunity protein im7 with an extended helix III===
+Amino acid insertion reveals a necessary three-helical intermediate in the folding pathway of the colicin E7 immunity protein Im7.,Knowling SE, Figueiredo AM, Whittaker SB, Moore GR, Radford SE J Mol Biol. 2009 Oct 2;392(4):1074-86. Epub 2009 Aug 3. PMID:19651139<ref>PMID:19651139</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2k0d" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19651139}}, adds the Publication Abstract to the page
+*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19651139 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19651139}}
+__TOC__
+</StructureSection>
-==About this Structure==
-K0D is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K0D OCA].
-==Reference==
-<ref group="xtra">PMID:19651139</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Figueiredo, A M.]]
+[[Category: Large Structures]]
-[[Category: Knowling, S E.]]
+[[Category: Figueiredo AM]]
-[[Category: Moore, G R.]]
+[[Category: Knowling SE]]
-[[Category: Radford, S E.]]
+[[Category: Moore GR]]
-[[Category: Spronk, C A.]]
+[[Category: Radford SE]]
-[[Category: Whittaker, S B.]]
+[[Category: Spronk CA]]
-[[Category: Protein]]
+[[Category: Whittaker SB]]
-[[Category: Toxin inhibitor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 30 14:24:39 2009''