Regulatory roles of the N-terminal domain based on crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands.
Pyruvate dehydrogenase kinase (PDHK) regulates the activity of the pyruvate dehydrogenase multienzyme complex. PDHK inhibition provides a route for therapeutic intervention in diabetes and cardiovascular disorders. We report crystal structures of human PDHK isozyme 2 complexed with physiological and synthetic ligands. Several of the PDHK2 structures disclosed have C-terminal cross arms that span a large trough region between the N-terminal regulatory (R) domains of the PDHK2 dimers. The structures containing bound ATP and ADP demonstrate variation in the conformation of the active site lid, residues 316-321, which enclose the nucleotide beta and gamma phosphates at the active site in the C-terminal catalytic domain. We have identified three novel ligand binding sites located in the R domain of PDHK2. Dichloroacetate (DCA) binds at the pyruvate binding site in the center of the R domain, which together with ADP, induces significant changes at the active site. Nov3r and AZ12 inhibitors bind at the lipoamide binding site that is located at one end of the R domain. Pfz3 (an allosteric inhibitor) binds in an extended site at the other end of the R domain. We conclude that the N-terminal domain of PDHK has a key regulatory function and propose that the different inhibitor classes act by discrete mechanisms. The structures we describe provide insights that can be used for structure-based design of PDHK inhibitors.
Knoechel
Thorsten R
TR
PGRD Sandwich, Pfizer Ltd, Sandwich, Kent CT139NJ, United Kingdom.
Tucker
Alec D
AD
Robinson
Colin M
CM
Phillips
Chris
C
Taylor
Wendy
W
Bungay
Peter J
PJ
Kasten
Shane A
SA
Roche
Thomas E
TE
Brown
David G
DG
D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D003999:Dichloroacetic Acid / Q000378:metabolism; D019281:Dimerization; D006801:Humans; D007527:Isoenzymes / Q000737:chemistry / Q000502:physiology; D008024:Ligands; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000502:physiology; D011485:Protein Binding; D011494:Protein Kinases / Q000737:chemistry* / Q000502:physiology*; D017346:Protein Serine-Threonine Kinases; D017434:Protein Structure, Tertiary; D000081382:Pyruvate Dehydrogenase Acetyl-Transferring Kinase; D014867:Water / Q000378:metabolism
D007527:Isoenzymes; D008024:Ligands; C000631430:PDK2 protein, human; D010446:Peptide Fragments; D000081382:Pyruvate Dehydrogenase Acetyl-Transferring Kinase; D014867:Water; D000255:Adenosine Triphosphate; D003999:Dichloroacetic Acid; D011494:Protein Kinases; D017346:Protein Serine-Threonine Kinases; D008274:Magnesium