1JEH

CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE

• PDB DOI: https://doi.org/10.2210/pdb1JEH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2001-06-18 Released: 2001-07-11 
• Deposition Author(s): Toyoda, T., Suzuki, K., Sekigushi, T., Reed, J., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast.

Toyoda, T., Suzuki, K., Sekiguchi, T., Reed, L.J., Takenaka, A.

(1998) J Biochem 123: 668-674

• PubMed: 9538259 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a021989
• Primary Citation of Related Structures:  
  1JEH


• PubMed Abstract: 
  

  The crystal structure of eucaryotic lipoamide dehydrogenase from yeast has been determined by an X-ray analysis at 2.7 (partially at 2.4) A resolution. The enzyme has two identical subunits related by a pseudo twofold symmetry. The tertiary structure is similar to those of other procaryotic enzymes. The active site, consisting of FAD, Cys44, and Cys49 from one subunit and His457' from the other subunit, is highly conserved. This enzyme is directly bound to the core protein E2 of the 2-oxoglutarate dehydrogenase complex, whereas it is bound to the pyruvate dehydrogenase complex through a protein X. The calculated electrostatic potential suggests two characteristic regions for binding with these two proteins.

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Organizational Affiliation: 

Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 104.82 kDa 
• Atom Count: 7,363 
• Modelled Residue Count: 956 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROLIPOAMIDE DEHYDROGENASE	A, B	478	Saccharomyces cerevisiae	Mutation(s): 0  EC: 1.8.1.4
UniProt
Find proteins for P09624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09624  Go to UniProtKB:  P09624

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.1	α = 90
b = 158.7	β = 90
c = 67.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
ROTAVATA	data reduction
MERLOT	phasing
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-11 
Deposition Author(s): Toyoda, T., Suzuki, K., Sekigushi, T., Reed, J., Takenaka, A.

Revision History  

• Version 1.0: 2001-07-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2018-02-07
  Changes: Experimental preparation
• Version 1.5: 2019-11-06
  Changes: Data collection, Database references
• Version 1.6: 2023-10-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.7: 2024-11-20
  Changes: Structure summary