3A7A

Crystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and apoH-protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 

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This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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, Japan. fujiwara@ier.tokushima-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipoate-protein ligase AA, C337Escherichia coli K-12Mutation(s): 0 
Gene Names: lplAyjjFb4386JW4349
EC: 6.3.4 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for P32099 (Escherichia coli (strain K12))
Explore P32099 
Go to UniProtKB:  P32099
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glycine cleavage system H proteinB, D128Escherichia coli K-12Mutation(s): 0 
Gene Names: gcvHb2904JW2872
UniProt
Find proteins for P0A6T9 (Escherichia coli (strain K12))
Explore P0A6T9 
Go to UniProtKB:  P0A6T9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
F [auth A], H [auth C]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
OCT
Query on OCT

Download Ideal Coordinates CCD File 
E [auth A], G [auth C]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.013α = 90
b = 102.016β = 90
c = 159.934γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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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: Advisory, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description