Structure and mechanism of a soluble diacylglycerol kinase

DgkB is an essential diacylglycerol kinase (Dgk) that participates in lipoteichoic acid biosynthesis in gram‐positive bacteria. The structure of Staphylococcus aureus DgkB, a prototypical member of the Dgk superfamily (Pfam00781) was solved both as the free enzyme and in complex with ADP. DgkB is an asymmetric dimer, and each monomer has nucleotide binding P‐loop in domain 1 located across from a second domain the presents the catalytic base and substrate to the active site. A distinctive feature of DkgB is the structural Mg 2+ site consisting of several conserved aspartate residues and structured water molecules. The enzyme requires both ATP•Mg 2+ plus free Mg 2+ for activity and site‐directed mutagenesis is consistent with the Asp•water•Mg 2+ network functioning to correctly orient the catalytic base, Glu273, in the active site. DgkB is activated and directed to membrane diacylglycerol through its interaction with anionic phospholipids. The nucleotide binding residues, the acidic amino acid ligands binding the structural Mg 2+ , and the active site base, Glu273, are conserved in the catalytic cores of the mammalian signaling Dgks, indicating that these enzymes use the same mechanism and have similar structures as DgkB. (Supported by NIH GM34496 and ALSAC)