1E24

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and ATP and MN2+

Summary for 1E24

• Entry DOI: 10.2210/pdb1e24/pdb
• Related: 1E1O 1E1T 1E22 1LYL
• Descriptor: LYSYL-TRNA SYNTHETASE, LYSINE, ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: ligase, aminoacyl-trna synthetase, protein biosynthesis
• Biological source: ESCHERICHIA COLI
• Cellular location: Cytoplasm: P14825
• Total number of polymer chains: 1
• Total formula weight: 58770.57

Authors

Desogus, G.,Todone, F.,Brick, P.,Onesti, S. (deposition date: 2000-05-16, release date: 2000-07-28, Last modification date: 2024-05-08)

Primary citation

Desogus, G.,Todone, F.,Brick, P.,Onesti, S.
Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction
Biochemistry, 39:8418-, 2000

PubMed Abstract: 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 alpha-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 A 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 Mn(2+). 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 alpha-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.

PubMed: 10913247
DOI: 10.1021/BI0006722

Experimental method

X-RAY DIFFRACTION (2.35 Å)