5FYA

Cubic crystal of the native PlpD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.141 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Lipid Targeting and Destruction by the Type V Secretion System of Pseudomonas Aeruginosa.

Da Mata Madeira, P.V.Zouhir, S.Basso, P.Neves, D.Laubier, A.Salacha, R.Bleves, S.Faudry, E.Contreras-Martel, C.Dessen, A.

(2016) J.Mol.Biol. 428: 1790

  • DOI: 10.1016/j.jmb.2016.03.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The type V secretion system is a macromolecular machine employed by a number of bacteria to secrete virulence factors into the environment. The human pathogen Pseudomonas aeruginosa employs the newly described type Vd secretion system to secrete a so ...

    The type V secretion system is a macromolecular machine employed by a number of bacteria to secrete virulence factors into the environment. The human pathogen Pseudomonas aeruginosa employs the newly described type Vd secretion system to secrete a soluble variant of PlpD, a lipase of the patatin-like family synthesized as a single macromolecule that also carries a polypeptide transport-associated domain and a 16-stranded β-barrel. Here we report the crystal structure of the secreted form of PlpD in its biologically active state. PlpD displays a classical lipase α/β hydrolase fold with a catalytic site located within a highly hydrophobic channel that entraps a lipidic molecule. The active site is covered by a flexible lid, as in other lipases, indicating that this region in PlpD must modify its conformation in order for catalysis at the water-lipid interface to occur. PlpD displays phospholipase A1 activity and is able to recognize a number of phosphatidylinositols and other phosphatidyl analogs. PlpD is the first example of an active phospholipase secreted through the type V secretion system, for which there are more than 200 homologs, revealing details of the lipid destruction arsenal expressed by P. aeruginosa in order to establish infection.


    Organizational Affiliation

    Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil; CNRS, IBS and BIG, Grenoble, France; CEA, IBS and BIG, Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France. Electronic address: andrea.dessen@ibs.fr.,Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil.,Univ. Grenoble Alpes, Bacterial Pathogenesis and Cellular Responses Group, Institut de Biosciences et Biotechnologies de Grenoble (BIG), Grenoble, France; CNRS, IBS and BIG, Grenoble, France; CEA, IBS and BIG, Grenoble, France; INSERM, UMR-S 1036 Biology of Cancer and Infection Laboratory, Grenoble, France.,CNRS, IBS and BIG, Grenoble, France; CEA, IBS and BIG, Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France. Electronic address: carlos.contreras@ibs.fr.,CNRS & Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PATATIN-LIKE PROTEIN, PLPD
A, B
314Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: plpD
Find proteins for Q9HYQ6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HYQ6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.141 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 145.906α = 90.00
b = 145.906β = 90.00
c = 145.906γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection