5JKI

Crystal structure of the first transmembrane PAP2 type phosphatidylglycerolphosphate phosphatase from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis.

Ghachi, M.E.Howe, N.Auger, R.Lambion, A.Guiseppi, A.Delbrassine, F.Manat, G.Roure, S.Peslier, S.Sauvage, E.Vogeley, L.Rengifo-Gonzalez, J.C.Charlier, P.Mengin-Lecreulx, D.Foglino, M.Touze, T.Caffrey, M.Kerff, F.

(2017) Cell. Mol. Life Sci. 74: 2319-2332

  • DOI: 10.1007/s00018-017-2464-6

  • PubMed Abstract: 
  • Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C <sub>55 </sub>-P) lipid carr ...

    Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C 55 -P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C 55 -PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 Å resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France.,Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland. martin.caffrey@tcd.ie.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France. thierry.touze@i2bc.paris-saclay.fr.,Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium.,Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.,Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium. fkerff@ulg.ac.be.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative lipid phosphate phosphatase YodM
A
222Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: pgpB (yodM)
EC: 3.1.3.27
Find proteins for O34349 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34349
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
WO4
Query on WO4

Download SDF File 
Download CCD File 
A
TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.066α = 90.00
b = 76.961β = 90.00
c = 99.629γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds de la Recherche Scientifique - FNRSBelgiumMIS # F.4518.12
BelspoBelgiumIAP # P7/44
Science Foundation IrelandIrelandgrant # 12/IA/1255

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references