Pyruvate Dehydrogenase Kinase-4 Structures Reveal a Metastable Open Conformation Fostering Robust Core-free Basal Activity

Wynn, R. Max; Kato, Masato; Chuang, Jacinta L.; Tso, Shih Chia; Li, Jun; Chuang, David T.

doi:10.1074/jbc.m802249200

Cited by 70 publications

(79 citation statements)

References 66 publications

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“…All inhibition titrations were performed at nine dose points ranging from 316 to 3.16 mM in a 3.162-fold dilution series, with each inhibitor concentration tested in duplicate. The remaining steps were described previously (39).…”

Section: Methodsmentioning

confidence: 99%

Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase

Tso¹,

Qi²,

Gui³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are elevated in maple syrup urine disease, heart failure, obesity, and type 2 diabetes. BCAA homeostasis is controlled by the mitochondrial branched-chain α-ketoacid dehydrogenase complex (BCKDC), which is negatively regulated by the specific BCKD kinase (BDK). Here, we used structure-based design to develop a BDK inhibitor, (S)-α-chloro-phenylpropionic acid [(S)-CPP]. Crystal structures of the BDK-(S)-CPP complex show that (S)-CPP binds to a unique allosteric site in the N-terminal domain, triggering helix movements in BDK. These conformational changes are communicated to the lipoyl-binding pocket, which nullifies BDK activity by blocking its binding to the BCKDC core. Administration of (S)-CPP to mice leads to the full activation and dephosphorylation of BCKDC with significant reduction in plasma BCAA concentrations. The results buttress the concept of targeting mitochondrial BDK as a pharmacological approach to mitigate BCAA accumulation in metabolic diseases and heart failure.branched-chain α-ketoacid dehydrogenase kinase inhibitor | structure-based inhibitor design | allosteric mechanisms | kinase-inhibitor complex structures | in vivo kinase inhibitor studies T he branched-chain amino acids (BCAA) leucine, isoleucine, and valine comprise 40% of essential amino acids in daily dietary intake (1). The catabolic pathways of BCAA begin with transamination by branched-chain aminotransferases giving rise to corresponding branch-chain α-ketoacids (BCKA). The second common step, the irreversible oxidative decarboxylation of BCKA, is catalyzed by the single mitochondrial branch-chain α-ketoacid dehydrogenase complex (BCKDC). The homeostasis of BCAA and BCKA in vivo is critical for health. The accumulation of BCAA and BCKA secondary to inherited BCKDC deficiency produces maple syrup urine disease (MSUD), which can lead to fatal acidosis, neurological derangement, and mental retardation (2, 3). In large-scale high-throughput metabolic profiling studies, high blood BCAA concentrations were found to be highly associated with the development of insulin resistance (4, 5) and can serve as useful metabolic markers in type 2 diabetes risk assessment (6, 7). Pathologic stresses produced by the accumulated BCKA are linked to congenital heart diseases and heart failure (8). The above findings underscore the pivotal role of aberrant BCAA metabolism in the pathogenesis of metabolic, cardiac, and neurological diseases.The 4.5-MDa human BCKDC consists of three catalytic components: a heterotetrameric (α 2 β 2 ) branched-chain α-ketoacid decarboxylase (E1), a homo-24 meric dihydrolipoyltransacylase (E2), and a homodimeric dihydrolipoamide dehydrogenase (E3). In addition, human BCKDC contains two regulatory enzymes: BCKD kinase (BDK) and BCKD phosphatase (BDP), the latter also called PP2Cm phosphatase; these enzymes tightly regulate activity of BCKDC through the phosphorylation (inactivation)/ dephosphorylation (activation) of the E1α subunits (9, 10). BCKDC is or...

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Section: Methodsmentioning

confidence: 99%

Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase

Tso¹,

Qi²,

Gui³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…Monomers in the dimeric PDK are in a headto-head orientation with the primary interaction between the C-terminal domains. In the absence of L2, PDK dimer forms a "closed" conformation, resulting in closing of the active-site cleft because of the disordered C-terminal tail of one monomer not interacting with the lipoyl-binding pocket of the opposite monomer (91)(92)(93). This conformation stabilizes the ATP lid and thus prevents dissociation of ADP, resulting in product inhibition.…”

Section: Regulation Of Pdch By Phosphorylationmentioning

confidence: 99%

“…The crystal structures of all four PDKs (either alone or in association with L2, ADP, or ATP) have been reported (87)(88)(89)(90)(91)(92)(93). Each PDK monomer has two domains of about equal size, the N-terminal domain and the C-terminal domain, and these two domains are connected by a flexible, poorly ordered loop.…”

Section: Regulation Of Pdch By Phosphorylationmentioning

confidence: 99%

The Pyruvate Dehydrogenase Complexes: Structure-based Function and Regulation

Patel

Nemeria

Furey

et al. 2014

Journal of Biological Chemistry

482

389

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The pyruvate dehydrogenase complexes (PDCs) from all known living organisms comprise three principal catalytic components for their mission: E1 and E2 generate acetyl-coenzyme A, whereas the FAD/NAD ؉ -dependent E3 performs redox recycling. Here we compare bacterial (Escherichia coli) and human PDCs, as they represent the two major classes of the superfamily of 2-oxo acid dehydrogenase complexes with different assembly of, and interactions among components. The human PDC is subject to inactivation at E1 by serine phosphorylation by four kinases, an inactivation reversed by the action of two phosphatases. Progress in our understanding of these complexes important in metabolism is reviewed.

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“…However, it remained unclear how this residue was critically involved in the catalytic function of PDK1. PDK1 has been known to interchange between two conformational states (24,(35)(36)(37). The closed conformation, where the C-terminal tail of each PDK1 subunit loses its interaction with the lipoyl-bearing domain (L2), has the active-site cleft closed inside.…”

Section: Covalent Modification By Jx06 Reduces Atp Affinity Of Pdk1mentioning

confidence: 99%

JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

et al. 2015

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Pyruvate dehydrogenase kinase PDK1 is a metabolic enzyme responsible for switching glucose metabolism from mitochondrial oxidation to aerobic glycolysis in cancer cells, a general hallmark of malignancy termed the Warburg effect. Herein we report the identification of JX06 as a selective covalent inhibitor of PDK1 in cells. JX06 forms a disulfide bond with the thiol group of a conserved cysteine residue (C240) based on recognition of a hydrophobic pocket adjacent to the ATP pocket of the PDK1 enzyme. Our investigations of JX06 mechanism suggested that covalent modification at C240 induced conformational changes at Arginine 286 through Van der Waals forces, thereby hindering access of ATP to its binding pocket and in turn impairing PDK1 enzymatic activity. Notably, cells with a higher dependency on glycolysis were more sensitive to PDK1 inhibition, reflecting a metabolic shift that promoted cellular oxidative stress and apoptosis. Our findings offer new mechanistic insights including how to therapeutically target PDK1 by covalently modifying the C240 residue. Cancer Res; 75(22); 4923-36. Ó2015 AACR.

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Pyruvate Dehydrogenase Kinase-4 Structures Reveal a Metastable Open Conformation Fostering Robust Core-free Basal Activity

Cited by 70 publications

References 66 publications

Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase

Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase

The Pyruvate Dehydrogenase Complexes: Structure-based Function and Regulation

JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

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