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 
  • R-Value Observed: 0.202 

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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
  • Primary Citation of Related Structures:  
    5JKI

  • 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 ...

    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. fkerff@ulg.ac.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative lipid phosphate phosphatase YodMA222Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yodMBSU19650pgpB
EC: 3.1.3 (PDB Primary Data), 3.1.3.27 (UniProt)
Membrane Entity: Yes 
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
C [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
WO4
Query on WO4

Download Ideal Coordinates CCD File 
B [auth A]TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
Unknown ligand
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 
  • 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
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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