1L8A

E. COLI PYRUVATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution.

Arjunan, P.Nemeria, N.Brunskill, A.Chandrasekhar, K.Sax, M.Yan, Y.Jordan, F.Guest, J.R.Furey, W.

(2002) Biochemistry 41: 5213-5221

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of the recombinant thiamin diphosphate-dependent E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined at a resolution of 1.85 A. The E. coli PDHc E1 component E1p is a homo ...

    The crystal structure of the recombinant thiamin diphosphate-dependent E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined at a resolution of 1.85 A. The E. coli PDHc E1 component E1p is a homodimeric enzyme and crystallizes with an intact dimer in an asymmetric unit. Each E1p subunit consists of three domains: N-terminal, middle, and C-terminal, with all having alpha/beta folds. The functional dimer contains two catalytic centers located at the interface between subunits. The ThDP cofactors are bound in the "V" conformation in clefts between the two subunits (binding involves the N-terminal and middle domains), and there is a common ThDP binding fold. The cofactors are completely buried, as only the C2 atoms are accessible from solution through the active site clefts. Significant structural differences are observed between individual domains of E1p relative to heterotetrameric multienzyme complex E1 components operating on branched chain substrates. These differences may be responsible for reported alternative E1p binding modes to E2 components within the respective complexes. This paper represents the first structural example of a functional pyruvate dehydrogenase E1p component from any species. It also provides the first representative example for the entire family of homodimeric (alpha2) E1 multienzyme complex components, and should serve as a model for this class of enzymes.


    Organizational Affiliation

    Biocrystallography Laboratory, Veterans Affairs Medical Center, P. O. Box 12055, University Drive C, Pittsburgh, Pennsylvania 15240, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate dehydrogenase E1 component
A, B
886Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aceE
EC: 1.2.4.1
Find proteins for P0AFG8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFG8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDP
Query on TDP

Download SDF File 
Download CCD File 
A, B
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.690α = 90.00
b = 141.600β = 102.40
c = 82.460γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-03-19 
  • Released Date: 2002-07-24 
  • Deposition Author(s): Furey, W., Arjunan, P.

Revision History 

  • Version 1.0: 2002-07-24
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance