2BU7 image
Entry Detail
PDB ID:
2BU7
Keywords:
Title:
crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2005-06-08
Release Date:
2006-02-02
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.24
R-Value Work:
0.21
Space Group:
P 64
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:PYRUVATE DEHYDROGENASE KINASE ISOENZYME 2
Chain IDs:A
Chain Length:394
Number of Molecules:1
Biological Source:HOMO SAPIENS
Ligand Molecules
Primary Citation
Regulatory Roles of the N-Terminal Domain Based on Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands.
Biochemistry 45 402 ? (2006)
PMID: 16401071 DOI: 10.1021/BI051402S

Abstact

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.

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