Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.02 kDa 
• Atom Count: 2889 
• Modelled Residue Count: 329 
• Deposited Residue Count: 347 
• Unique protein chains: 1

2E5A

Crystal Structure of Bovine Lipoyltransferase in Complex with Lipoyl-AMP

• PDB DOI: 10.2210/pdb2E5A/pdb

• Classification: LIGASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-19 Released: 2007-09-04 
• Deposition Author(s): Fujiwara, K., Hosaka, H., Matsuda, M., Suzuki, M., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Crystal structure of bovine Lipoyltransferase in complex with lipoyl-AMP

Fujiwara, K., Hosaka, H., Matsuda, M., Okamura-Ikeda, K., Motokawa, Y., Suzuki, M., Nakagawa, A., Taniguchi, H.

(2007) J Mol Biol 371: 222-234

• PubMed: 17570395 
• DOI: 10.1016/j.jmb.2007.05.059
• Primary Citation of Related Structures:  
  2E5A


• PubMed Abstract: 
  

Lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system. It is covalently attached to a specific lysine residue of the subunit of the complexes. The bovine lipoyltransferase (bLT) catalyzes the lipoic acid attachment reaction using lipoyl-AMP as a substrate, forming a lipoylated protein and AMP. To gain insights into the reaction mechanism at the atomic level, we have determined the crystal structure of bLT at 2.10 A resolution. Unexpectedly, the purified recombinant bLT contains endogenous lipoyl-AMP. The structure of bLT consists of N-terminal and C-terminal domains, and lipoyl-AMP is bound to the active site in the N-terminal domain, adopting a U-shaped conformation. The lipoyl moiety is buried in the hydrophobic pocket, forming van der Waals interactions, and the AMP moiety forms numerous hydrogen bonds with bLT in another tunnel-like cavity. These interactions work together to expose the C10 atom of lipoyl-AMP to the surface of the bLT molecule. The carbonyl oxygen atom of lipoyl-AMP interacts with the invariant Lys135. The interaction might stimulate the positive charge of the C10 atom of lipoyl-AMP, and consequently facilitate the nucleophilic attack by the lysine residue of the lipoate-acceptor protein, accompanying the bond cleavage between the carbonyl group and the phosphate group. We discuss the structural differences between bLT and the lipoate-protein ligase A from Escherichia coli and Thermoplasma acidophilum. We further demonstrate that bLT in mitochondria also contains endogenous lipoylmononucleotide, being ready for the lipoylation of apoproteins.

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Organizational Affiliation: 

Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoyltransferase 1	A	347	Bos taurus	Mutation(s): 0  Gene Names: LIPT1 EC: 6 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for O46419 (Bos taurus) Explore O46419  Go to UniProtKB:  O46419

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LAQ	E [auth A]	5'-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE C18 H26 N5 O8 P S2 QWEGOCJRZOKSOE-ADUAKINBSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACY	F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.439	α = 90
b = 81.439	β = 90
c = 120.532	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-19 
• Released Date: 2007-09-04 
Deposition Author(s): Fujiwara, K., Hosaka, H., Matsuda, M., Suzuki, M., Nakagawa, A.

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance