Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.00 kDa 
• Atom Count: 2293 
• Modelled Residue Count: 267 
• Deposited Residue Count: 272 
• Unique protein chains: 1

4UHQ

Crystal structure of the pyocin AP41 DNase

• PDB DOI: 10.2210/pdb4UHQ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-25 Released: 2015-08-05 
• Deposition Author(s): Joshi, A., Chen, S., Wojdyla, J.A., Kaminska, R., Kleanthous, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.191 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

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

• PubMed: 26215615 
• DOI: 10.1016/j.jmb.2015.07.014
• Primary Citation of Related Structures:  
  4UHP, 4UHQ


• 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 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LARGE COMPONENT OF PYOCIN AP41	A, B	136	Pseudomonas aeruginosa PAO1	Mutation(s): 0
UniProt
Find proteins for Q51502 (Pseudomonas aeruginosa) Explore Q51502  Go to UniProtKB:  Q51502

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth A], F [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
NI	E [auth A], G [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.191 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.575	α = 90
b = 100.575	β = 90
c = 71.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-25 
• Released Date: 2015-08-05 
Deposition Author(s): Joshi, A., Chen, S., Wojdyla, J.A., Kaminska, R., Kleanthous, C.

Revision History  

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