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| | ==How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor== | | ==How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor== |
| - | <StructureSection load='1znv' size='340' side='right' caption='[[1znv]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='1znv' size='340' side='right'caption='[[1znv]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1znv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecow3 Ecow3]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZNV FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mz8|1mz8]], [[1pt3|1pt3]], [[7cei|7cei]], [[1m08|1m08]]</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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cei7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316407 ECOW3])</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=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> |
| - | <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=1znv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1znv OCA], [http://pdbe.org/1znv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1znv RCSB], [http://www.ebi.ac.uk/pdbsum/1znv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1znv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. [[http://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_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/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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1znv" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1znv" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Colicin 3D structures|Colicin 3D structures]] |
| | + | *[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecow3]] | + | [[Category: Escherichia coli str. K-12 substr. W3110]] |
| - | [[Category: Doudeva, L G]] | + | [[Category: Large Structures]] |
| - | [[Category: Hsia, K C]] | + | [[Category: Doudeva LG]] |
| - | [[Category: Huang, H]] | + | [[Category: Hsia KC]] |
| - | [[Category: Li, C L]] | + | [[Category: Huang H]] |
| - | [[Category: Shen, Y]] | + | [[Category: Li CL]] |
| - | [[Category: Shi, Z]] | + | [[Category: Shen Y]] |
| - | [[Category: Yuan, H S]] | + | [[Category: Shi Z]] |
| - | [[Category: Endonuclease]]
| + | [[Category: Yuan HS]] |
| - | [[Category: H-n-h motif]]
| + | |
| - | [[Category: Hydrolase-protein binding complex]]
| + | |
| - | [[Category: Ni-binding]]
| + | |
| - | [[Category: Protein-protein complex]]
| + | |
| Structural highlights
Function
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
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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 <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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y, Cheng YS, Yuan HS. Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+. Protein Sci. 2006 Feb;15(2):269-80. PMID:16434744 doi:15/2/269
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