Substrate induced structural and dynamics changes in human phosphomevalonate kinase and implications for mechanism

Area of Science:

• Biochemistry
• Enzymology
• Structural Biology

Background:

• Phosphomevalonate kinase (PMK) is vital for isoprenoid and steroid synthesis, catalyzing ATP-dependent phosphorylation of mevalonate 5-phosphate.
• The enzyme's active site presents a challenge due to high negative charge density, necessitating specific conformational dynamics for catalysis.

Purpose of the Study:

• To characterize substrate-induced conformational and dynamics changes in PMK using NMR spectroscopy.
• To elucidate the mechanism of Michaelis complex formation and identify key residues involved in catalysis.

Main Methods:

• NMR-based dynamics and chemical shift perturbation measurements were employed.
• Analysis of substrate binding (Mg-ADP, M5P) and ternary complex formation in PMK.

Main Results:

• Substrate binding induces distinct structural changes: M5P binding compresses PMK, while Mg-ADP binding opens it.
• NMR data identified potential hinge residues (H55, R93, D163) involved in domain movements.
• Binding of M5P rigidifies catalytic residues, though some slower timescale motion persists.

Conclusions:

• PMK utilizes domain closure around a hinge region upon M5P binding to facilitate catalysis.
• The N-terminus is disordered, suggesting a potential regulatory or signal peptide role.
• Enzyme dynamics provide insights into the catalytic mechanism of PMK in isoprenoid biosynthesis.