Hydrogen bonding pathways in human dihydroorotate dehydrogenase

Area of Science:

• Biochemistry
• Enzymology
• Molecular Biology

Background:

• Dihydroorotate dehydrogenase (DHOD) is a key enzyme in pyrimidine biosynthesis, catalyzing a critical redox reaction.
• The enzyme's mechanism involves proton and hydride transfer, with a proposed proton relay system in the active site.

Purpose of the Study:

• To identify and characterize potential hydrogen bonding pathways in human DHOD using molecular dynamics simulations.
• To investigate the impact of active site serine mutation on these pathways and enzyme activity.

Main Methods:

• * Molecular dynamics (MD) simulations were employed to analyze the active site of human DHOD.
• * The study focused on identifying hydrogen bonding networks facilitating proton and hydride transfer.
• * The effects of mutating the active base serine to cysteine were simulated and analyzed.

Main Results:

• * MD simulations revealed specific hydrogen bonding pathways involving active site serine, water molecules, and substrate/threonine residues.
• * These pathways facilitate proton transfer from the substrate to the bulk solvent.
• * Mutation of serine to cysteine increased donor-acceptor distances and disrupted the identified hydrogen bonding pathways.

Conclusions:

• * The identified hydrogen bonding pathways are essential for the catalytic activity of human DHOD.
• Mutating the active serine residue significantly impairs these pathways, leading to reduced enzyme function.
• These findings provide insights into the enzyme's mechanism and the consequences of active site modifications.