5JKI

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

Summary for 5JKI

• Entry DOI: 10.2210/pdb5jki/pdb
• Descriptor: Putative lipid phosphate phosphatase YodM, TUNGSTATE(VI)ION, (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, ... (5 entities in total)
• Functional Keywords: transmembrane pap2, phophatidylglycerol phosphate phosphatase, hydrolase
• Biological source: Bacillus subtilis (strain 168)
• Cellular location: Cell membrane ; Multi-pass membrane protein : O34349
• Total number of polymer chains: 1
• Total formula weight: 25760.21

Authors

El Ghachi, M.,Howe, N.,Lampion, A.,Delbrassine, F.,Vogeley, L.,Caffrey, M.,Sauvage, E.,Auger, R.,Guiseppe, A.,Roure, S.,Perlier, S.,Mengin-lecreulx, D.,Foglino, M.,Touze, T. (deposition date: 2016-04-26, release date: 2017-02-22, Last modification date: 2025-10-01)

Primary citation

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.
Crystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis.
Cell. Mol. Life Sci., 74:2319-2332, 2017

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-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-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.

PubMed: 28168443
DOI: 10.1007/s00018-017-2464-6

Experimental method

X-RAY DIFFRACTION (2.25 Å)