Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP

Experimental Data Snapshot

  • Resolution: 2.03 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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

Wynn, R.M.Kato, M.Chuang, J.L.Tso, S.C.Li, J.Chuang, D.T.

(2008) J Biol Chem 283: 25305-25315

  • DOI: https://doi.org/10.1074/jbc.M802249200
  • Primary Citation of Related Structures:  
    2ZKJ, 3D2R

  • PubMed Abstract: 

    Human pyruvate dehydrogenase complex (PDC) is down-regulated by pyruvate dehydrogenase kinase (PDK) isoforms 1-4. PDK4 is overexpressed in skeletal muscle in type 2 diabetes, resulting in impaired glucose utilization. Here we show that human PDK4 has robust core-free basal activity, which is considerably higher than activity levels of other PDK isoforms stimulated by the PDC core. PDK4 binds the L3 lipoyl domain, but its activity is not significantly stimulated by any individual lipoyl domains or the core of PDC. The 2.0-A crystal structures of the PDK4 dimer with bound ADP reveal an open conformation with a wider active-site cleft, compared with that in the closed conformation epitomized by the PDK2-ADP structure. The open conformation in PDK4 shows partially ordered C-terminal cross-tails, in which the conserved DW (Asp(394)-Trp(395)) motif from one subunit anchors to the N-terminal domain of the other subunit. The open conformation fosters a reduced binding affinity for ADP, facilitating the efficient removal of product inhibition by this nucleotide. Alteration or deletion of the DW-motif disrupts the C-terminal cross-tail anchor, resulting in the closed conformation and the nearly complete inactivation of PDK4. Fluorescence quenching and enzyme activity data suggest that compounds AZD7545 and dichloroacetate lock PDK4 in the open and the closed conformational states, respectively. We propose that PDK4 with bound ADP exists in equilibrium between the open and the closed conformations. The favored metastable open conformation is responsible for the robust basal activity of PDK4 in the absence of the PDC core.

  • Organizational Affiliation

    Department of Biochemistry, Dallas, Texas 75390-9038; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4
A, B
394Homo sapiensMutation(s): 0 
Gene Names: PDK4
UniProt & NIH Common Fund Data Resources
Find proteins for Q16654 (Homo sapiens)
Explore Q16654 
Go to UniProtKB:  Q16654
PHAROS:  Q16654
GTEx:  ENSG00000004799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16654
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.03 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.595α = 90
b = 69.374β = 99.26
c = 82.328γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description