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 PQS (software)

Macromolecule Content

• Total Structure Weight: 211.07 kDa 
• Atom Count: 13374 
• Residue Count: 1619 
• Unique protein chains: 2

2JGD

E. COLI 2-oxoglutarate dehydrogenase (E1o)

• DOI: 10.2210/pdb2JGD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-12 Released: 2007-02-27 
• Deposition Author(s): Frank, R.A.W., Price, A.J., Northrop, F.D., Perham, R.N., Luisi, B.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Crystal Structure of the E1 Component of the Escherichia Coli 2-Oxoglutarate Dehydrogenase Multienzyme Complex.

Frank, R.A.W., Price, A.J., Northrop, F.D., Perham, R.N., Luisi, B.F.

(2007) J Mol Biol 368: 639

• PubMed: 17367808 
• DOI: 10.1016/j.jmb.2007.01.080
• Primary Citation of Related Structures:  
  2JGD


• PubMed Abstract: 
  

The thiamine-dependent E1o component (EC 1.2.4.2) of the 2-oxoglutarate dehydrogenase complex catalyses a rate-limiting step of the tricarboxylic acid cycle (TCA) of aerobically respiring organisms. We describe the crystal structure of Escherichia coli E1o in its apo and holo forms at 2.6 A and 3.5 A resolution, respectively. The structures reveal the characteristic fold that binds thiamine diphosphate and resemble closely the alpha(2)beta(2) hetero-tetrameric E1 components of other 2-oxo acid dehydrogenase complexes, except that in E1o, the alpha and beta subunits are fused as a single polypeptide. The extended segment that links the alpha-like and beta-like domains forms a pocket occupied by AMP, which is recognised specifically. Also distinctive to E1o are N-terminal extensions to the core fold, and which may mediate interactions with other components of the 2-oxoglutarate dehydrogenase multienzyme complex. The active site pocket contains a group of three histidine residues and one serine that appear to confer substrate specificity and the capacity to accommodate the TCA metabolite oxaloacetate. Oxaloacetate inhibits E1o activity at physiological concentrations, and we suggest that the inhibition may allow coordinated activity within the TCA cycle. We discuss the implications for metabolic control in facultative anaerobes, and for energy homeostasis of the mammalian brain.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT	A	933	Escherichia coli K-12	Mutation(s): 0  Gene Names: sucA, b0726, JW0715 EC: 1.2.4.2
Find proteins for P0AFG3 (Escherichia coli (strain K12)) Explore P0AFG3  Go to UniProtKB:  P0AFG3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT	B	933	Escherichia coli K-12	Mutation(s): 0  Gene Names: sucA, b0726, JW0715 EC: 1.2.4.2
Find proteins for P0AFG3 (Escherichia coli (strain K12)) Explore P0AFG3  Go to UniProtKB:  P0AFG3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	A, B	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.493	α = 90
b = 142.493	β = 90
c = 251.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-12 
• Released Date: 2007-02-27 
Deposition Author(s): Frank, R.A.W., Price, A.J., Northrop, F.D., Perham, R.N., Luisi, B.F.

Revision History 

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other