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 

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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Colicin-E9 immunity protein
A, D
86Escherichia coliMutation(s): 7 
Gene Names: imm (ceiE9)
Find proteins for P13479 (Escherichia coli)
Go to UniProtKB:  P13479
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin-E7
B, C
141Escherichia coliMutation(s): 1 
Gene Names: colE7 (cea)
EC: 3.1.-.-
Find proteins for Q47112 (Escherichia coli)
Go to UniProtKB:  Q47112
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download 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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.650α = 90.00
b = 53.713β = 105.59
c = 79.334γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2013-03-27
    Type: Experimental preparation