Crystal Structure of Lipate-Protein Ligase A from Escherichia coli complexed with lipoic acid

Experimental Data Snapshot

  • Resolution: 2.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

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Crystal structure of lipoate-protein ligase A from Escherichia coli: Determination of the lipoic acid-binding site

Fujiwara, K.Toma, S.Okamura-Ikeda, K.Motokawa, Y.Nakagawa, A.Taniguchi, H.

(2005) J Biol Chem 280: 33645-33651

  • DOI: https://doi.org/10.1074/jbc.M505010200
  • Primary Citation of Related Structures:  
    1X2G, 1X2H

  • PubMed Abstract: 

    Lipoate-protein ligase A (LplA) catalyzes the formation of lipoyl-AMP from lipoate and ATP and then transfers the lipoyl moiety to a specific lysine residue on the acyltransferase subunit of alpha-ketoacid dehydrogenase complexes and on H-protein of the glycine cleavage system. The lypoyllysine arm plays a pivotal role in the complexes by shuttling the reaction intermediate and reducing equivalents between the active sites of the components of the complexes. We have determined the X-ray crystal structures of Escherichia coli LplA alone and in a complex with lipoic acid at 2.4 and 2.9 angstroms resolution, respectively. The structure of LplA consists of a large N-terminal domain and a small C-terminal domain. The structure identifies the substrate binding pocket at the interface between the two domains. Lipoic acid is bound in a hydrophobic cavity in the N-terminal domain through hydrophobic interactions and a weak hydrogen bond between carboxyl group of lipoic acid and the Ser-72 or Arg-140 residue of LplA. No large conformational change was observed in the main chain structure upon the binding of lipoic acid.

  • Organizational Affiliation

    Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan. fujiwara@ier.tokushima-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoate-protein ligase A
A, B, C
337Escherichia coliMutation(s): 5 
EC: 6.3.2
Find proteins for P32099 (Escherichia coli (strain K12))
Explore P32099 
Go to UniProtKB:  P32099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32099
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C
Experimental Data & Validation

Experimental Data

  • Resolution: 2.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.2α = 90
b = 111.6β = 90
c = 289.6γ = 90
Software Package:
Software NamePurpose
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: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description