Crystal structure of E. coli lipoate-protein ligase A in complex with lipoyl-AMP.

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A.

Fujiwara, K.Maita, N.Hosaka, H.Okamura-Ikeda, K.Nakagawa, A.Taniguchi, H.

(2010) J Biol Chem 285: 9971-9980

  • DOI: https://doi.org/10.1074/jbc.M109.078717
  • Primary Citation of Related Structures:  
    3A7A, 3A7L, 3A7R, 3A7U

  • PubMed Abstract: 

    Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645-33651). Here, we report two new LplA structures, LplA.lipoyl-5'-AMP and LplA.octyl-5'-AMP.apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5'-AMP reaction intermediate and rotation of the C-terminal domain by about 180 degrees . These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys(133) residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes.

  • Organizational Affiliation

    Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503. Electronic address: fujiwara@ier.tokushima-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoate-protein ligase A337Escherichia coli K-12Mutation(s): 0 
Gene Names: lplAyjjFb4386JW4349
EC: 6.3.4
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.298α = 90
b = 102.298β = 90
c = 221.252γ = 120
Software Package:
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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description