4KT3

Structure of a type VI secretion system effector-immunity complex from Pseudomonas protegens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4362 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification, Structure, and Function of a Novel Type VI Secretion Peptidoglycan Glycoside Hydrolase Effector-Immunity Pair.

Whitney, J.C.Chou, S.Russell, A.B.Biboy, J.Gardiner, T.E.Ferrin, M.A.Brittnacher, M.Vollmer, W.Mougous, J.D.

(2013) J.Biol.Chem. 288: 26616-26624

  • DOI: 10.1074/jbc.M113.488320

  • PubMed Abstract: 
  • Bacteria employ type VI secretion systems (T6SSs) to facilitate interactions with prokaryotic and eukaryotic cells. Despite the widespread identification of T6SSs among Gram-negative bacteria, the number of experimentally validated substrate effector ...

    Bacteria employ type VI secretion systems (T6SSs) to facilitate interactions with prokaryotic and eukaryotic cells. Despite the widespread identification of T6SSs among Gram-negative bacteria, the number of experimentally validated substrate effector proteins mediating these interactions remains small. Here, employing an informatics approach, we define novel families of T6S peptidoglycan glycoside hydrolase effectors. Consistent with the known intercellular self-intoxication exhibited by the T6S pathway, we observe that each effector gene is located adjacent to a hypothetical open reading frame encoding a putative periplasmically localized immunity determinant. To validate our sequence-based approach, we functionally investigate a representative family member from the soil-dwelling bacterium Pseudomonas protegens. We demonstrate that this protein is secreted in a T6SS-dependent manner and that it confers a fitness advantage in growth competition assays with Pseudomonas putida. In addition, we determined the 1.4 Å x-ray crystal structure of this effector in complex with its cognate immunity protein. The structure reveals the effector shares highest overall structural similarity to a glycoside hydrolase family associated with peptidoglycan N-acetylglucosaminidase activity, suggesting that T6S peptidoglycan glycoside hydrolase effector families may comprise significant enzymatic diversity. Our structural analyses also demonstrate that self-intoxication is prevented by the immunity protein through direct occlusion of the effector active site. This work significantly expands our current understanding of T6S effector diversity.


    Organizational Affiliation

    From the Departments of Microbiology and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A
177Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)Mutation(s): 0 
Find proteins for Q4KC90 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Go to UniProtKB:  Q4KC90
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative lipoprotein
B
137Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)Mutation(s): 0 
Find proteins for Q4KC91 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Go to UniProtKB:  Q4KC91
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4362 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.112α = 90.00
b = 81.515β = 90.00
c = 86.453γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2013-10-09
    Type: Database references