Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 111917.95 
• Atom Count: 7223 
• Residue Count: 988 
• Unique protein chains: 2

3CRK

Crystal structure of the PDHK2-L2 complex.

• DOI: 10.2210/pdb3CRK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2008-04-07 Released: 2008-04-29 
• Deposition Author(s): Green, T.J., Popov, K.M., Luo, M., Grigorian, A., Klyuyeva, A., Tuganova, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 

Literature

Structural and functional insights into the molecular mechanisms responsible for the regulation of pyruvate dehydrogenase kinase 2.

Green, T., Grigorian, A., Klyuyeva, A., Tuganova, A., Luo, M., Popov, K.M.

(2008) J.Biol.Chem. 283: 15789-15798

• PubMed: 18387944 
• DOI: 10.1074/jbc.M800311200
• Primary Citation of Related Structures:  
  3CRL


• PubMed Abstract: 
  

PDHK2 is a mitochondrial protein kinase that phosphorylates pyruvate dehydrogenase complex, thereby down-regulating the oxidation of pyruvate. Here, we present the crystal structure of PDHK2 bound to the inner lipoyl-bearing domain of dihydrolipoamide transacetylase (L2) determined with or without bound adenylyl imidodiphosphate. Both structures reveal a PDHK2 dimer complexed with two L2 domains. Comparison with apo-PDHK2 shows that L2 binding causes rearrangements in PDHK2 structure that affect the L2- and E1-binding sites. Significant differences are found between PDHK2 and PDHK3 with respect to the structure of their lipoyllysine-binding cavities, providing the first structural support to a number of studies showing that these isozymes are markedly different with respect to their affinity for the L2 domain. Both structures display a novel type II potassium-binding site located on the PDHK2 interface with the L2 domain. Binding of potassium ion at this site rigidifies the interface and appears to be critical in determining the strength of L2 binding. Evidence is also presented that potassium ions are indispensable for the cross-talk between the nucleotide- and L2-binding sites of PDHK2. The latter is believed to be essential for the movement of PDHK2 along the surface of the transacetylase scaffold.

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Organizational Affiliation: 

Department of Microbiology, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial	A, B	407	Rattus norvegicus	Mutation(s): 0  Gene Names: Pdk2 EC: 2.7.11.2
Find proteins for Q64536 (Rattus norvegicus) Go to UniProtKB:  Q64536

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial	C, D	87	Homo sapiens	Mutation(s): 0  Gene Names: DLAT (DLTA) EC: 2.3.1.12
Find proteins for P10515 (Homo sapiens) Go to Gene View: DLAT Go to UniProtKB:  P10515

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A, B	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LA2	C, D	L-peptide linking	C14 H28 N2 O3 S2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.380	α = 90.00
b = 120.679	β = 96.03
c = 71.466	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	refinement
COMO	phasing
MAR345	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-07 
• Released Date: 2008-04-29 
• Deposition Author(s): Green, T.J., Popov, K.M., Luo, M., Grigorian, A., Klyuyeva, A., Tuganova, A.

Revision History 

• Version 1.0: 2008-04-29
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Type: Refinement description