Sequential magnesium binding facilitates lysyl-tRNA synthetase to recognize ATP

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that attach amino acids to their cognate tRNAs, a process requiring ATP and magnesium ions.
• Class II aaRSs, like lysyl-tRNA synthetase (LysRS), bind ATP with multiple magnesium ions, but the precise role of magnesium in ATP recognition remains unclear.

Purpose of the Study:

• To elucidate the mechanism by which magnesium ions facilitate ATP recognition by class II aaRSs.
• To investigate intermediate states of ATP binding in human LysRS.

Main Methods:

• Analysis of crystal structures of human LysRS.
• Comparison with previously solved LysRS structures.
• Investigation of enzyme active sites in different ATP-bound states.

Main Results:

• Human LysRS crystal structures revealed distinct states of ATP and magnesium binding in the enzyme's active sites.
• Only one magnesium ion was observed bound, even in intermediate ATP-recognition states, differing from the expected three.
• A proposed order for the sequential binding of three magnesium ions was established.
• Multiple intermediate ATP-bound states were identified, offering insights into the reaction mechanism.

Conclusions:

• The study provides critical insights into the magnesium-dependent mechanism of ATP binding and activation by class II aaRSs.
• The findings clarify the role of magnesium ions in LysRS function and offer a basis for understanding other related enzymes.