2BTZ

crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Regulatory Roles of the N-Terminal Domain Based on Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands.

Knoechel, T.R.Tucker, A.D.Robinson, C.M.Phillips, C.Taylor, W.Bungay, P.J.Kasten, S.A.Roche, T.E.Brown, D.G.

(2006) Biochemistry 45: 402

  • DOI: 10.1021/bi051402s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 hum ...

    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.


    Organizational Affiliation

    PGRD Sandwich, Pfizer Ltd, Sandwich, Kent CT139NJ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE DEHYDROGENASE KINASE ISOENZYME 2
A
394Homo sapiensMutation(s): 0 
Gene Names: PDK2 (PDHK2)
EC: 2.7.11.2
Find proteins for Q15119 (Homo sapiens)
Go to Gene View: PDK2
Go to UniProtKB:  Q15119
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.266 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 109.317α = 90.00
b = 109.317β = 90.00
c = 85.087γ = 120.00
Software Package:
Software NamePurpose
HKLdata reduction
SCALEPACKdata scaling
CNXrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance