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2erh

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Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7 DNAse and the Im7 immunity protein

Structural highlights

2erh is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 redesign of protein-protein interactions is a stringent test of our understanding of molecular recognition and specificity. Previously we engineered a modest specificity switch into the colicin E7 DNase-Im7 immunity protein complex by identifying mutations that are disruptive in the native complex, but can be compensated by mutations on the interacting partner. Here we extend the approach by systematically sampling alternate rigid body orientations to optimize the interactions in a binding mode specific manner. Using this protocol we designed a de novo hydrogen bond network at the DNase-immunity protein interface and confirmed the design with X-ray crystallographic analysis. Subsequent design of the second shell of interactions guided by insights from the crystal structure on tightly bound water molecules, conformational strain, and packing defects yielded new binding partners that exhibited specificities of at least 300-fold between the cognate and the non-cognate complexes. This multi-step approach should be applicable to the design of polar protein-protein interactions and contribute to the re-engineering of regulatory networks mediated by protein-protein interactions.

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.,Joachimiak LA, Kortemme T, Stoddard BL, Baker D J Mol Biol. 2006 Aug 4;361(1):195-208. Epub 2006 May 24. PMID:16831445^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Joachimiak LA, Kortemme T, Stoddard BL, Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol. 2006 Aug 4;361(1):195-208. Epub 2006 May 24. PMID:16831445 doi:10.1016/j.jmb.2006.05.022

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2erh"

@@ Line 3: / Line 3: @@
 <StructureSection load='2erh' size='340' side='right'caption='[[2erh]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2erh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ERH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ERH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2erh]] is a 2 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=2ERH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ERH FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7cei|7cei]]</div></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]] 2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">imm, ceiE7 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), colE7, cea ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2erh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2erh OCA], [https://pdbe.org/2erh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2erh RCSB], [https://www.ebi.ac.uk/pdbsum/2erh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2erh 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. [[https://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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Baker, D]]
+[[Category: Baker D]]
-[[Category: Joachimiak, L A]]
+[[Category: Joachimiak LA]]
-[[Category: Kortemme, T]]
+[[Category: Kortemme T]]
-[[Category: Stoddard, B L]]
+[[Category: Stoddard BL]]
-[[Category: Computational design]]
-[[Category: Hydrogen bond network]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Molecular recognition]]
-[[Category: Protein complex]]
-[[Category: Redesigned protein-protein interface]]
-[[Category: Specificity]]

2erh

From Proteopedia

Current revision

Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7 DNAse and the Im7 immunity protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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