1X2H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1074/jbc.M505010200
  • Primary Citation of Related Structures:  1X2G

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoate-protein ligase A
A, B, C
337Escherichia coli (strain K12)Gene Names: lplA (yjjF)
EC: 6.3.1.20
Find proteins for P32099 (Escherichia coli (strain K12))
Go to UniProtKB:  P32099
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LPA
Query on LPA

Download SDF File 
Download CCD File 
A, B
LIPOIC ACID
5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid
C8 H14 O2 S2
AGBQKNBQESQNJD-SSDOTTSWSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 83.200α = 90.00
b = 111.600β = 90.00
c = 289.600γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description