E. coli Pyruvate dehydrogenase E1 component E401K mutant with phosphonolactylthiamin diphosphate

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.232 

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This is version 1.4 of the entry. See complete history


A Dynamic Loop at the Active Center of the Escherichia coli Pyruvate Dehydrogenase Complex E1 Component Modulates Substrate Utilization and Chemical Communication with the E2 Component

Kale, S.Arjunan, P.Furey, W.Jordan, F.

(2007) J Biol Chem 282: 28106-28116

  • DOI: https://doi.org/10.1074/jbc.M704326200
  • Primary Citation of Related Structures:  
    2QTA, 2QTC

  • PubMed Abstract: 

    Our crystallographic studies have shown that two active center loops (an inner loop formed by residues 401-413 and outer loop formed by residues 541-557) of the E1 component of the Escherichia coli pyruvate dehydrogenase complex become organized only on binding a substrate analog that is capable of forming a stable thiamin diphosphate-bound covalent intermediate. We showed that residue His-407 on the inner loop has a key role in the mechanism, especially in the reductive acetylation of the E. coli dihydrolipoamide transacetylase component, whereas crystallographic results showed a role of this residue in a disorder-order transformation of these two loops, and the ordered conformation gives rise to numerous new contacts between the inner loop and the active center. We present mapping of the conserved residues on the inner loop. Kinetic, spectroscopic, and crystallographic studies on some inner loop variants led us to conclude that charged residues flanking His-407 are important for stabilization/ordering of the inner loop thereby facilitating completion of the active site. The results further suggest that a disorder to order transition of the dynamic inner loop is essential for substrate entry to the active site, for sequestering active site chemistry from undesirable side reactions, as well as for communication between the E1 and E2 components of the E. coli pyruvate dehydrogenase multienzyme complex.

  • Organizational Affiliation

    Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate dehydrogenase E1 component
A, B
886Escherichia coliMutation(s): 1 
Gene Names: aceE
Find proteins for P0AFG8 (Escherichia coli (strain K12))
Explore P0AFG8 
Go to UniProtKB:  P0AFG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFG8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TDK

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C15 H26 N4 O11 P3 S
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.77 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.61α = 90
b = 142.11β = 102.68
c = 82.14γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-15
    Changes: Structure summary
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description