3GJN

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Following evolutionary paths to protein-protein interactions with high affinity and selectivity

Levin, K.B., Dym, O., Albeck, S., Magdassi, S., Keeble, A.H., Kleanthous, C., Tawfik, D.S.

(2009) Nat Struct Mol Biol 16: 1049-1055

  • DOI: 10.1038/nsmb.1670
  • Primary Citation of Related Structures:  
    3GJN

  • PubMed Abstract: 

    • How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evo ...

    How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evolved it toward ColE7, which it inhibits promiscuously (Kd > 10(-8) M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity (against ColE9 inhibition), led to an approximately 10(5)-fold increase in affinity and a 10(8)-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.

    Organizational Affiliation: 

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Colicin-E9 immunity protein A, D86Escherichia coliMutation(s): 7 
Gene Names: imm, ceiE9
Find proteins for P13479 (Escherichia coli)
Explore P13479 
Go to UniProtKB:  P13479
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Colicin-E7 B, C141Escherichia coliMutation(s): 1 
Gene Names: colE7, cea
EC: 3.1
Find proteins for Q47112 (Escherichia coli)
Explore Q47112 
Go to UniProtKB:  Q47112
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.65α = 90
b = 53.713β = 105.59
c = 79.334γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-03-09 
  • Released Date: 2009-09-15 
    • Deposition Author(s): Dym, O., Tawfik, D.S.

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-03-27
    Changes: Experimental preparation