2WPT

The crystal structure of Im2 in complex with colicin E9 DNase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structural and Energetic Basis for High Selectivity in a High-Affinity Protein-Protein Interaction.

Meenan, N.A.Sharma, A.Fleishman, S.J.Macdonald, C.J.Morel, B.Boetzel, R.Moore, G.R.Baker, D.Kleanthous, C.

(2010) Proc.Natl.Acad.Sci.USA 107: 10080

  • DOI: 10.1073/pnas.0910756107

  • PubMed Abstract: 
  • High-affinity, high-selectivity protein-protein interactions that are critical for cell survival present an evolutionary paradox: How does selectivity evolve when acquired mutations risk a lethal loss of high-affinity binding? A detailed understandin ...

    High-affinity, high-selectivity protein-protein interactions that are critical for cell survival present an evolutionary paradox: How does selectivity evolve when acquired mutations risk a lethal loss of high-affinity binding? A detailed understanding of selectivity in such complexes requires structural information on weak, noncognate complexes which can be difficult to obtain due to their transient and dynamic nature. Using NMR-based docking as a guide, we deployed a disulfide-trapping strategy on a noncognate complex between the colicin E9 endonuclease (E9 DNase) and immunity protein 2 (Im2), which is seven orders of magnitude weaker binding than the cognate femtomolar E9 DNase-Im9 interaction. The 1.77 A crystal structure of the E9 DNase-Im2 complex reveals an entirely noncovalent interface where the intersubunit disulfide merely supports the crystal lattice. In combination with computational alanine scanning of interfacial residues, the structure reveals that the driving force for binding is so strong that a severely unfavorable specificity contact is tolerated at the interface and as a result the complex becomes weakened through "frustration." As well as rationalizing past mutational and thermodynamic data, comparing our noncognate structure with previous cognate complexes highlights the importance of loop regions in developing selectivity and accentuates the multiple roles of buried water molecules that stabilize, ameliorate, or aggravate interfacial contacts. The study provides direct support for dual-recognition in colicin DNase-Im protein complexes and shows that weakened noncognate complexes are primed for high-affinity binding, which can be achieved by economical mutation of a limited number of residues at the interface.


    Organizational Affiliation

    Department of Biology, P.O. Box 373, University of York, York, YO10 5YW, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLICIN-E2 IMMUNITY PROTEIN
A
86Escherichia coliMutation(s): 2 
Gene Names: imm (ceiB)
Find proteins for P04482 (Escherichia coli)
Go to UniProtKB:  P04482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COLICIN-E9
B
134Escherichia coliMutation(s): 1 
Gene Names: col (cei)
EC: 3.1.-.-
Find proteins for P09883 (Escherichia coli)
Go to UniProtKB:  P09883
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.229α = 90.00
b = 82.897β = 90.00
c = 89.528γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance