4UHP

Crystal structure of the pyocin AP41 DNase-Immunity complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the Ultra-High Affinity Protein-Protein Complexes of Pyocins S2 and Ap41 and Their Cognate Immunity Proteins from Pseudomonas Aeruginosa

Joshi, A.Grinter, R.Josts, I.Chen, S.Wojdyla, J.A.Lowe, E.D.Kaminska, R.Sharp, C.Mccaughey, L.Roszak, A.W.Cogdell, R.J.Byron, O.Walker, D.Kleanthous, C.

(2015) J.Mol.Biol. 427: 2852

  • DOI: 10.1016/j.jmb.2015.07.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • How ultra-high-affinity protein-protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential ...

    How ultra-high-affinity protein-protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential for the neutralisation of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The colicin DNase-Im interaction is a model system for the study of high-affinity protein-protein interactions. However, despite the fact that closely related colicin-like bacteriocins are widely produced by Gram-negative bacteria, this interaction has only been studied using colicins from Escherichia coli. In this work, we present the first crystal structures of two pyocin DNase-Im complexes from Pseudomonas aeruginosa, pyocin S2 DNase-ImS2 and pyocin AP41 DNase-ImAP41. These structures represent divergent DNase-Im subfamilies and are important in extending our understanding of protein-protein interactions for this important class of high-affinity protein complex. A key finding of this work is that mutations within the immunity protein binding energy hotspot, helix III, are tolerated by complementary substitutions at the DNase-Immunity protein binding interface. Im helix III is strictly conserved in colicins where an Asp forms polar interactions with the DNase backbone. ImAP41 contains an Asp-to-Gly substitution in helix III and our structures show the role of a co-evolved substitution where Pro in DNase loop 4 occupies the volume vacated and removes the unfulfilled hydrogen bond. We observe the co-evolved mutations in other DNase-Immunity pairs that appear to underpin the split of this family into two distinct groups.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LARGE COMPONENT OF PYOCIN AP41
A, C, E, G
136Pseudomonas aeruginosaMutation(s): 0 
Find proteins for Q51502 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q51502
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BACTERIOCIN IMMUNITY PROTEIN
B, D, F, H
98Pseudomonas aeruginosaMutation(s): 0 
Find proteins for Q51503 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q51503
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.604α = 79.19
b = 75.627β = 78.05
c = 83.171γ = 77.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references