1znv: Difference between revisions

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-{{Seed}}
-[[Image:1znv.png|left|200px]]
-<!--
+==How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor==
-The line below this paragraph, containing "STRUCTURE_1znv", creates the "Structure Box" on the page.
+<StructureSection load='1znv' size='340' side='right'caption='[[1znv]], [[Resolution|resolution]] 2.00&Aring;' 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'>[[1znv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._W3110 Escherichia coli str. K-12 substr. W3110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZNV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZNV 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">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_1znv|  PDB=1znv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1znv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1znv OCA], [https://pdbe.org/1znv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1znv RCSB], [https://www.ebi.ac.uk/pdbsum/1znv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1znv ProSAT]</span></td></tr>
+</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/zn/1znv_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=1znv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The nuclease domain of ColE7 (N-ColE7) contains an H-N-H motif that folds in a beta beta alpha-metal topology. Here we report the crystal structures of a Zn2+-bound N-ColE7 (H545E mutant) in complex with a 12-bp duplex DNA and a Ni2+-bound N-ColE7 in complex with the inhibitor Im7 at a resolution of 2.5 A and 2.0 A, respectively. Metal-dependent cleavage assays showed that N-ColE7 cleaves double-stranded DNA with a single metal ion cofactor, Ni2+, Mg2+, Mn2+, and Zn2+. ColE7 purified from Escherichia coli contains an endogenous zinc ion that was not replaced by Mg2+ at concentrations of &lt;25 mM, indicating that zinc is the physiologically relevant metal ion in N-ColE7 in host E. coli. In the crystal structure of N-ColE7/DNA complex, the zinc ion is directly coordinated to three histidines and the DNA scissile phosphate in a tetrahedral geometry. In contrast, Ni2+ is bound in N-ColE7 in two different modes, to four ligands (three histidines and one phosphate ion), or to five ligands with an additional water molecule. These data suggest that the divalent metal ion in the His-metal finger motif can be coordinated to six ligands, such as Mg2+ in I-PpoI, Serratia nuclease and Vvn, five ligands or four ligands, such as Ni2+ or Zn2+ in ColE7. Universally, the metal ion in the His-metal finger motif is bound to the DNA scissile phosphate and serves three roles during hydrolysis: polarization of the P-O bond for nucleophilic attack, stabilization of the phosphoanion transition state and stabilization of the cleaved product.
-===How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor===
+Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+.,Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y, Cheng YS, Yuan HS Protein Sci. 2006 Feb;15(2):269-80. PMID:16434744<ref>PMID:16434744</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1znv" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16434744}}, adds the Publication Abstract to the page
+*[[Colicin 3D structures|Colicin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16434744 is the PubMed ID number.
+*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_16434744}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-ZNV is a 4 chains structure of sequences 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=1ZNV OCA].
+[[Category: Escherichia coli str. K-12 substr. W3110]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Doudeva LG]]
-<ref group="xtra">PMID:16434744</ref><references group="xtra"/>
+[[Category: Hsia KC]]
-[[Category: Escherichia coli]]
+[[Category: Huang H]]
-[[Category: Doudeva, L G.]]
+[[Category: Li CL]]
-[[Category: Hsia, K C.]]
+[[Category: Shen Y]]
-[[Category: Huang, H.]]
+[[Category: Shi Z]]
-[[Category: Li, C L.]]
+[[Category: Yuan HS]]
-[[Category: Shen, Y.]]
-[[Category: Shi, Z.]]
-[[Category: Yuan, H S.]]
-[[Category: Endonuclease]]
-[[Category: H-n-h motif]]
-[[Category: Ni-binding]]
-[[Category: Protein-protein complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:39:47 2009''