Structure of rat BCKD kinase: Nucleotide-induced domain communication in amitochondrial protein kinase

Mitochondrial protein kinases (mPKs) are molecular switches that down-regul ate the oxidation of branched-chain a-ketoacids and pyruvate. Elevated leve ls of these metabolites are implicated in disease states such as insulin-re sistant Type II diabetes, branched-chain ketoaciduria, and primary lactic a cidosis. We report a three-dimensional structure of a member of the mPK fam ily, rat branched-chain a-ketoacid dehydrogenase kinase (BCK). BCK features a characteristic nucleotide-binding domain and a four-helix bundle domain. These two domains are reminiscent of modules found in protein histidine ki nases (PHKs), which are involved in two-component signal transduction syste ms. Unlike PHKs, BCK dimerizes through direct interaction of two opposing n ucleotide-binding domains. Nucleotide binding to BCK is uniquely mediated b y both potassium and magnesium. Binding of ATP induces disorder-order trans itions in a loop region at the nucleotide-binding site. These structural ch anges lead to the formation of a quadruple aromatic stack in the interface between the nucleotide-binding domain and the four-helix bundle domain, whe re they induce a movement of the top portion of two helices. Phosphotransfe r induces further ordering of the loop region, effectively trapping the rea ction product ADP, which explains product inhibition in mPKs. The BCK struc ture is a prototype for all mPKs and will provide a framework for structure -assisted inhibitor design for this family of kinases.