1JEH

CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


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

  • DOI: 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 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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROLIPOAMIDE DEHYDROGENASEA, B478Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.8.1.4
UniProt
Find proteins for P09624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P09624 
Go to UniProtKB:  P09624
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.1α = 90
b = 158.7β = 90
c = 67.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
ROTAVATAdata reduction
MERLOTphasing
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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