Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 104.34 kDa 
• Atom Count: 7668 
• Residue Count: 942 
• Unique protein chains: 1

4JDR

Dihydrolipoamide dehydrogenase of pyruvate dehydrogenase from escherichia coli

• DOI: 10.2210/pdb4JDR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-25 Released: 2013-04-24 
• Deposition Author(s): Chandrasekhar, K., Arjunan, P., Furey, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Insight to the Interaction of the Dihydrolipoamide Acetyltransferase (E2) Core with the Peripheral Components in the Escherichia coli Pyruvate Dehydrogenase Complex via Multifaceted Structural Approaches.

Chandrasekhar, K., Wang, J., Arjunan, P., Sax, M., Park, Y.H., Nemeria, N.S., Kumaran, S., Song, J., Jordan, F., Furey, W.

(2013) J Biol Chem 288: 15402-15417

• PubMed: 23580650 
• DOI: 10.1074/jbc.M113.466789
• Primary Citation of Related Structures:  
  4JDR


• PubMed Abstract: 
  

Multifaceted structural approaches were undertaken to investigate interaction of the E2 component with E3 and E1 components from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), as a representative of the PDHc from Gram-negative bacteria. The crystal structure of E3 at 2.5 Å resolution reveals similarity to other E3 structures and was an important starting point for understanding interaction surfaces between E3 and E2. Biochemical studies revealed that R129E-E2 and R150E-E2 substitutions in the peripheral subunit-binding domain (PSBD) of E2 greatly diminished PDHc activity, affected interactions with E3 and E1 components, and affected reductive acetylation of E2. Because crystal structures are unavailable for any complete E2-containing complexes, peptide-specific hydrogen/deuterium exchange mass spectrometry was used to identify loci of interactions between 3-lipoyl E2 and E3. Two peptides from the PSBD, including Arg-129, and three peptides from E3 displayed statistically significant reductions in deuterium uptake resulting from interaction between E3 and E2. Of the peptides identified on E3, two were from the catalytic site, and the third was from the interface domain, which for all known E3 structures is believed to interact with the PSBD. NMR clearly demonstrates that there is no change in the lipoyl domain structure on complexation with E3. This is the first instance where the entire wild-type E2 component was employed to understand interactions with E3. A model for PSBD-E3 binding was independently constructed and found to be consistent with the importance of Arg-129, as well as revealing other electrostatic interactions likely stabilizing this complex.

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Organizational Affiliation: 

Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	474	Escherichia coli	Mutation(s): 0  Gene Names: lpdA, lpd, b0116, JW0112 EC: 1.8.1.4
Find proteins for P0A9P0 (Escherichia coli (strain K12)) Explore P0A9P0  Go to UniProtKB:  P0A9P0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MES	A, B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180	α = 90
b = 180	β = 90
c = 196.9	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-25 
• Released Date: 2013-04-24 
Deposition Author(s): Chandrasekhar, K., Arjunan, P., Furey, W.

Revision History 

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references