Crystal Structure of an Asymmetric Complex of Pyruvate Dehydrogenase Kinase 3 with Lipoyl Domain 2 and its Biological Implications

Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine and Dentistry, Kaul Genetics Building, Birmingham, Al 35294, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 08/2007; 370(3):407-16. DOI: 10.1016/j.jmb.2007.04.083
Source: PubMed


A homodimer of pyruvate dehydrogenase kinase (PDHK) is an integral part of pyruvate dehydrogenase complex (PDC) to which it is anchored primarily through the inner lipoyl-bearing domains (L2) of transacetylase component. The catalytic cycle of PDHK and its translocation over the PDC surface is thought to be mediated by the "symmetric" and "asymmetric" modes, in which the PDHK dimer binds to two and one L2-domain(s), respectively. Whereas the structure of the symmetric PDHK/L2 complex was reported, the structural organization and functional role of the asymmetric complex remain obscure. Here, we report the crystal structure of the asymmetric PDHK3/L2 complex that reveals several functionally important features absent from the previous structures. First, the PDHK3 subunits have distinct conformations: one subunit exhibits "open" and the other "closed" configuration of the putative substrate-binding cleft. Second, access to the closed cleft is additionally restricted by local unwinding of the adjacent alpha-helix. Modeling indicates that the target peptide might gain access to the PDHK active center through the open but not through the closed cleft. Third, the ATP-binding loop in one PDHK3 subunit adopts an open conformation, implying that the nucleotide loading into the active site is mediated by the inactive "pre-insertion" binding mode. Altogether our data suggest that the asymmetric complex represents a physiological state in which binding of a single L2-domain activates one of the PDHK protomers while inactivating another. Thus, the L2-domains likely act not only as the structural anchors but also modulate the catalytic cycle of PDHK.

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Available from: Yancho Devedjiev, Jun 23, 2015
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    • "The segment between helices α6 and α7 forms part of the active-site cleft of PDK1; therefore, the unwound conformation in this segment, as a result of DCA binding, may also decrease kinase activity by thwarting the binding of the E1p substrate to the kinase. In this context, the structure of an asymmetric PDK3-L2 complex harboring only one bound L2 domain has been recently reported (Devedjiev et al., 2007). In this structure, a corresponding unwound " loopingout " segment is present in the L2-bound subunit of the PDK3 dimer, resulting in narrowing of the active-site cleft by 6 Å in the same subunit. "
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