Active Site of Lysyl-tRNA Synthetase:  Structural Studies of the Adenylation Reaction

• Published in: Biochemistry (Easton) Vol. 39; no. 29; pp. 8418 - 8425
• Main Authors: Desogus, Gianluigi, Todone, Flavia, Brick, Peter, Onesti, Silvia
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 25.07.2000
• Subjects: Adenosine Triphosphate - analogs & derivatives; Adenosine Triphosphate - metabolism; Amino Acid Sequence; Amino Acyl-tRNA Synthetases - genetics; Catalytic Domain; Crystallography, X-Ray; Escherichia coli; Escherichia coli - enzymology; Escherichia coli - genetics; Ligands; Lysine - metabolism; Lysine-tRNA Ligase - chemistry; Lysine-tRNA Ligase - genetics; Lysine-tRNA Ligase - metabolism; LysU protein; Models, Molecular; Molecular Sequence Data; Protein Conformation; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Sequence Homology, Amino Acid; Static Electricity
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi0006722

Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA. The energy required for the formation of the ester bond between the amino acid carboxylate group and the tRNA acceptor stem is supplied by coupling the reaction to the hydrolysis of ATP. Lysyl-tRNA synthetase from Escherichia coli belongs to the family of class II synthetases and carries out a two-step reaction, in which lysine is activated by being attached to the α-phosphate of AMP before being transferred to the cognate tRNA. Crystals of the thermo-inducible E. coli lysyl-tRNA synthetase LysU which diffract to 2.1 Å resolution have been used to determine crystal structures of the enzyme in the presence of lysine, the lysyl−adenylate intermediate, and the nonhydrolyzable ATP analogue AMP-PCP. Additional data have been obtained from crystals soaked in a solution containing ATP and Mn2+. The refined crystal structures give “snapshots” of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP α-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilize the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding.