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2vlp

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Revision as of 11:39, 30 March 2022

R54A mutant of E9 DNase domain in complex with Im9

Structural highlights

2vlp is a 2 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2ivz, 1v14, 1fsj, 1v15, 1bxi, 1imp, 1imq, 1v13, 1e0h, 1emv, 1fr2, 2vln, 2vlo, 2vlq
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Colicin endonucleases (DNases) are bound and inactivated by immunity (Im) proteins. Im proteins are broadly cross-reactive yet specific inhibitors binding cognate and non-cognate DNases with K(d) values that vary between 10(-4) and 10(-14) M, characteristics that are explained by a 'dual-recognition' mechanism. In this work, we addressed for the first time the energetics of Im protein recognition by colicin DNases through a combination of E9 DNase alanine scanning and double-mutant cycles (DMCs) coupled with kinetic and calorimetric analyses of cognate Im9 and non-cognate Im2 binding, as well as computational analysis of alanine scanning and DMC data. We show that differential DeltaDeltaGs observed for four E9 DNase residues cumulatively distinguish cognate Im9 association from non-cognate Im2 association. E9 DNase Phe86 is the primary specificity hotspot residue in the centre of the interface, which is coordinated by conserved and variable hotspot residues of the cognate Im protein. Experimental DMC analysis reveals that only modest coupling energies to Im9 residues are observed, in agreement with calculated DMCs using the program ROSETTA and consistent with the largely hydrophobic nature of E9 DNase-Im9 specificity contacts. Computed values for the 12 E9 DNase alanine mutants showed reasonable agreement with experimental DeltaDeltaG data, particularly for interactions not mediated by interfacial water molecules. DeltaDeltaG predictions for residues that contact buried water molecules calculated using solvated rotamer models met with mixed success; however, we were able to predict with a high degree of accuracy the location and energetic contribution of one such contact. Our study highlights how colicin DNases are able to utilise both conserved and variable amino acids to distinguish cognate from non-cognate Im proteins, with the energetic contributions of the conserved residues modulated by neighbouring specificity sites.

Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases.,Keeble AH, Joachimiak LA, Mate MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C J Mol Biol. 2008 Jun 13;379(4):745-59. Epub 2008 Apr 3. PMID:18471830^[1]

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

References

↑ Keeble AH, Joachimiak LA, Mate MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C. Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. J Mol Biol. 2008 Jun 13;379(4):745-59. Epub 2008 Apr 3. PMID:18471830 doi:http://dx.doi.org/10.1016/j.jmb.2008.03.055

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/2vlp"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vlp' size='340' side='right'caption='[[2vlp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vlp]] is a 2 chain structure with sequence from [http://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=2VLP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VLP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vlp]] 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=2VLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLP FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ivz|2ivz]], [[1v14|1v14]], [[1fsj|1fsj]], [[1v15|1v15]], [[1bxi|1bxi]], [[1imp|1imp]], [[1imq|1imq]], [[1v13|1v13]], [[1e0h|1e0h]], [[1emv|1emv]], [[1fr2|1fr2]], [[2vln|2vln]], [[2vlo|2vlo]], [[2vlq|2vlq]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ivz|2ivz]], [[1v14|1v14]], [[1fsj|1fsj]], [[1v15|1v15]], [[1bxi|1bxi]], [[1imp|1imp]], [[1imq|1imq]], [[1v13|1v13]], [[1e0h|1e0h]], [[1emv|1emv]], [[1fr2|1fr2]], [[2vln|2vln]], [[2vlo|2vlo]], [[2vlq|2vlq]]</div></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vlp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vlp OCA], [http://pdbe.org/2vlp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vlp RCSB], [http://www.ebi.ac.uk/pdbsum/2vlp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vlp ProSAT]</span></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=2vlp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vlp OCA], [https://pdbe.org/2vlp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vlp RCSB], [https://www.ebi.ac.uk/pdbsum/2vlp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vlp 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.
+[[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]]

2vlp

From Proteopedia

Revision as of 11:39, 30 March 2022

R54A mutant of E9 DNase domain in complex with Im9

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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