2QV7

Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg

Summary for 2QV7

• Entry DOI: 10.2210/pdb2qv7/pdb
• Related: 2QVL
• Descriptor: Diacylglycerol Kinase DgkB, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: alpha-beta domain 1, beta sandwich domain 2, protein-adp complex, transferase
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 1
• Total formula weight: 38350.74

Authors

Miller, D.J.,Jerga, A.,Rock, C.O.,White, S.W. (deposition date: 2007-08-07, release date: 2008-06-17, Last modification date: 2024-11-20)

Primary citation

Miller, D.J.,Jerga, A.,Rock, C.O.,White, S.W.
Analysis of the Staphylococcus aureus DgkB Structure Reveals a Common Catalytic Mechanism for the Soluble Diacylglycerol Kinases.
Structure, 16:1036-1046, 2008

PubMed Abstract: Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg2+ site and an associated Asp*water*Mg2+ network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp*water*Mg2+ network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB.

PubMed: 18611377
DOI: 10.1016/j.str.2008.03.019

Experimental method

X-RAY DIFFRACTION (2.3 Å)