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PDB:2C8M

Protein Name

Lipoate protein ligase A (LplA)

Species

Thermoplasma acidophilum (archaea,thermophile)

Biological Context

Lipoic acid is a crucial prosthetic group which is important in various enzymatic reactions, especially in the metabolic reactions; oxidative decarboxylation of 2-oxo acids, glycine cleavage, and so on. Lipoic acid is attached in the amide linkage to the N6-aminogroup of a lysine residue in the enzyme as a lipoyl group. The long lipoyl-lysine chain can catalyze a lot of reactions, and if lipoyl group does not exist in the enzyme, the enzyme is inactive. The lipoyl modification of the enzyme occurs after translation. This reaction is catalyzed by lipoate protein ligase (Lpl). Some bacterial and mammalian Lpls have been found, but in many archaea, Lpls have not been identified. Because the proteins of archea, especially of thermophilc organisms, are amenable to crystallization, they are good samples for structure analysis. Some research groups performed BLAST search with E. coli LplA, the gene and the protein structure of which are well known, as a query to seek archaea Lpls. This revealed a potential homologue in T. acidphilum, Ta0514. They assumed that Ta0514 is T. acidphilum LplA and analyzed the crystal structure.

Structure Description

2c8m2c8m_x2c8m_y

T. acidphilum LplA belongs to alpha/beta class proteins, which consists of a central parallel or mixed beta-sheet surrounded by alpha-helices. Lipoic acid is accommodated in a pocket formed by the central beta-sheet, the helix labeled H1 and the three short beta-strands labeled B4, and bind to V79, I46, R72, N87 and H161. While these amino acid residues are conserved in the Lpl family, the comparison of the lipoic acid binding site between the E. coli and T. acidphilum enzymes shows the lipoic acid to be bound in different areas. The significance of this difference remains to be elucidated. It is proposed that LplAs are structurally similar to biotin protein ligases, Birs. Then comparison of the structures in the substrate binding site between T. acidphilum LplA and E.coli BirA was performed. This revealed that lipoic acid and biotin within the two enzymes occupy almost identical position. However, biotin cannot bind to LplA, and lipoic acid cannot bind to BirA despite their structural similarity. How does this difference arise? This is not fully understood but this specificity is considered to derive from the two loop structures in each enzymes. These loops are also found in E. coli LplA. In T. acidphilum LplA, the loops correspond 71-79 and 179-193. In the first loop, G77 forms a bifurcated hydrogen bond with R72. This forms an attractive surface for lipoic acid to interact with. The second loop is disordered when the substrate is unbound and the important residues are unknown. But this loop is thought to play a key role in ligand binding and/or catalysis because the loops are located near the substrate binding site and are superimposed. Although the structure of T. acidphilum LplA and E. coli LplA are very similar and share two flexible loops, T. acidphilum LplA does not have C-terminal region of E. coli LplA. Then BLAST search was performed with C-terminal region of E. coli LplA as a query. A 10 kDa protein of T. acidphilum, Ta0513 found. Interestingly, this gene is located next to the Ta0154, LplA, on the genome of T. acidphilum. When Ta0513 sequence was analyzed by a distant homology detection method, the C-terminal region of the S. pneumoniae LplA structure was matched with high degree of confidence, suggesting that these proteins are functionally equivalent. These results implied that lipoylation in T. acidphilum requires two enzymes to catalyze two-part reaction; one catalyzes the activation of lipoic acid to lipoyl-AMP, the other catalyzes the transfer of the lipoyl group to apo-lipoyl domain.

Protein Data Bank (PDB)

References

Source

  • Mcmanus, E. Luisi, B.F. Perham, R.N.; "Structure of a Putative Lipoate Protein Ligase from Thermoplasma Acidophilum and the Mechanism of Target Selection for Post-Translational Modification."; J. Mol. Biol.; (2006) 356:625-637 PubMed:16384580.

Others

author: Daisuke Ino


Japanese version:PDB:2C8M