Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 63.30 kDa 
• Atom Count: 3949 
• Residue Count: 478 
• Unique protein chains: 2

1Y8P

Crystal structure of the PDK3-L2 complex

• DOI: 10.2210/pdb1Y8P/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-12-13 Released: 2005-05-24 
• Deposition Author(s): Kato, M., Chuang, J.L., Wynn, R.M., Chuang, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.230 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex.

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

(2005) EMBO J 24: 1763-1774

• PubMed: 15861126 
• DOI: 10.1038/sj.emboj.7600663
• Primary Citation of Related Structures:  
  1Y8O, 1Y8N, 1Y8P


• PubMed Abstract: 
  

The human pyruvate dehydrogenase complex (PDC) is regulated by reversible phosphorylation by four isoforms of pyruvate dehydrogenase kinase (PDK). PDKs phosphorylate serine residues in the dehydrogenase (E1p) component of PDC, but their amino-acid sequences are unrelated to eukaryotic Ser/Thr/Tyr protein kinases. PDK3 binds to the inner lipoyl domains (L2) from the 60-meric transacetylase (E2p) core of PDC, with concomitant stimulated kinase activity. Here, we present crystal structures of the PDK3-L2 complex with and without bound ADP or ATP. These structures disclose that the C-terminal tail from one subunit of PDK3 dimer constitutes an integral part of the lipoyl-binding pocket in the N-terminal domain of the opposing subunit. The two swapped C-terminal tails promote conformational changes in active-site clefts of both PDK3 subunits, resulting in largely disordered ATP lids in the ADP-bound form. Our structural and biochemical data suggest that L2 binding stimulates PDK3 activity by disrupting the ATP lid, which otherwise traps ADP, to remove product inhibition exerted by this nucleotide. We hypothesize that this allosteric mechanism accounts, in part, for E2p-augmented PDK3 activity.

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Organizational Affiliation: 

Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3	A	419	Homo sapiens	Mutation(s): 0  Gene Names: PDK3, PDHK3 EC: 2.7.1.99 (PDB Primary Data), 2.7.11.2 (UniProt)
Find proteins for Q15120 (Homo sapiens) Explore Q15120  Go to UniProtKB:  Q15120
NIH Common Fund Data Resources
PHAROS:  Q15120 GTEx:  ENSG00000067992

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	B	128	Homo sapiens	Mutation(s): 0  Gene Names: DLAT, DLTA EC: 2.3.1.12
Find proteins for P10515 (Homo sapiens) Explore P10515  Go to UniProtKB:  P10515
NIH Common Fund Data Resources
PHAROS:  P10515 GTEx:  ENSG00000150768

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
RED	B	DIHYDROLIPOIC ACID C8 H16 O2 S2 IZFHEQBZOYJLPK-SSDOTTSWSA-N
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ATP	Kd :  840   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.230 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.904	α = 90
b = 120.904	β = 90
c = 240.085	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-13 
• Released Date: 2005-05-24 
Deposition Author(s): Kato, M., Chuang, J.L., Wynn, R.M., Chuang, D.T.

Revision History 

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-10-05
  Changes: Non-polymer description