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

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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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: https://doi.org/10.1007/s00018-017-2464-6
  • Primary Citation of Related Structures:  

  • 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 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

    Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative lipid phosphate phosphatase YodM222Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yodMBSU19650
EC: 3.1.3
Membrane Entity: Yes 
Find proteins for O34349 (Bacillus subtilis (strain 168))
Explore O34349 
Go to UniProtKB:  O34349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34349
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.066α = 90
b = 76.961β = 90
c = 99.629γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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  (Full details and data files)

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