Pyruvate dehydrogenase kinase 2 (PDK2) is a prototypical mitochondrial protein kinase that regulates the activity of the pyruvate dehydrogenase complex. Recent structural studies have established that PDK2 consists of a catalytic core built of the B and K domains and the relatively long amino and carboxyl tails of unknown function. Here, we show that the carboxy-terminal truncation variants of PDK2 display a greatly diminished capacity for phosphorylation of holo-PDC. This effect is due largely to the inability of the transacetylase component of PDC to promote the phosphorylation reaction catalyzed by the truncated PDK2 variants. Furthermore, the truncated forms of PDK2 bind poorly to the lipoyl-bearing domain(s) provided by the transacetylase component. Taken together, these data strongly suggest that the carboxyl tails of PDK isozymes contribute to the lipoyl-bearing domain-binding site of the kinase molecule. We also show that the carboxyl tails derived from isozymes PDK1, PDK3, and PDK4 are capable of supporting the kinase activity of the kinase core derived from PDK2 as well as binding of the respective PDK2 chimeras to the lipoylbearing domain. Furthermore, the chimera carrying the carboxyl tail of PDK3 displays a stronger response to the addition of the transacetylase component along with a better binding to the lipoylbearing domain, suggesting that, at least in part, the differences in the amino acid sequences of the carboxyl tails account for the differences between PDK isozymes.Mammalian mitochondria harbor four closely related protein kinases (isozymes PDK1-PDK4) 1 that regulate the activity of the pyruvate dehydrogenase complex (PDC) (1-3) and thereby control the disposal rates of pyruvate and of other metabolically related three-carbon compounds (4).It is generally believed that at least three of the four isozymes (PDK1-PDK3) are the integral components of a multienzyme complex (3,5). On average, PDC contains just two to three kinase molecules per complex (6). A growing body of evidence strongly suggests that the kinase molecule uses the so-called lipoyl-bearing domains (LBDs) as docking sites for the attachment to the complex (7-9). In PDC, there are three types of LBDs (LBD1-LBD3) (10). Two of those domains (LBD1 and LBD2) are provided by the acetyltransferase component of the complex (E2) (11), and one (LBD3) is provided by the so-called E3-binding protein (E3BP) (12), which is a structural component of PDC tightly integrated with E2 (E2-E3BP subcomplex) (10). LBD2 is thought to be the primary binding site for the kinase molecule (13). Kinase activities