2E5A

Crystal Structure of Bovine Lipoyltransferase in Complex with Lipoyl-AMP

Summary for 2E5A

• Entry DOI: 10.2210/pdb2e5a/pdb
• Descriptor: Lipoyltransferase 1, MAGNESIUM ION, PHOSPHATE ION, ... (6 entities in total)
• Functional Keywords: lipoyltransferase, lipoyl-amp, ligase
• Biological source: Bos taurus (cattle)
• Cellular location: Mitochondrion: O46419
• Total number of polymer chains: 1
• Total formula weight: 40024.63

Authors

Fujiwara, K.,Hosaka, H.,Matsuda, M.,Suzuki, M.,Nakagawa, A. (deposition date: 2006-12-19, release date: 2007-09-04, Last modification date: 2024-03-13)

Primary citation

Fujiwara, K.,Hosaka, H.,Matsuda, M.,Okamura-Ikeda, K.,Motokawa, Y.,Suzuki, M.,Nakagawa, A.,Taniguchi, H.
Crystal structure of bovine Lipoyltransferase in complex with lipoyl-AMP
J.Mol.Biol., 371:222-234, 2007

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.

PubMed: 17570395
DOI: 10.1016/j.jmb.2007.05.059

Experimental method

X-RAY DIFFRACTION (2.1 Å)