A Density Functional Study of Active Site Models for Xanthine Oxidase

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Xanthine oxidase (XnO) is a crucial enzyme in purine metabolism.
• The coordination of ligands to the molybdenum active site is key to XnO function.
• Previous studies suggested hydroxide coordination, but theoretical validation was needed.

Purpose of the Study:

• To theoretically investigate the coordination of hydroxide to the oxidized molybdenum site in xanthine oxidase.
• To compare different coordination numbers (four, five, and six) and ligand types.
• To validate theoretical models against experimental Extended X-ray Absorption Fine Structure (EXAFS) data.

Main Methods:

• Density Functional Theory (DFT) using the local density approximation.
• Modeling of dithiolene and thiolate sulfur ligands.
• Computation of active site models with varying coordination numbers and ligands.
• Comparison of computed molybdenum-ligand (M-L) distances with EXAFS data.

Main Results:

• Four- and six-coordinate models showed M-S bond lengths inconsistent with EXAFS data.
• Five-coordinate models with hydroxide (X = [OH]-) exhibited excellent agreement between computed and experimental M-L distances.
• Models with water, ammonia, thiolate, or oxide ligands showed poor agreement.

Conclusions:

• The theoretical findings strongly support hydroxide coordination to the molybdenum site in xanthine oxidase.
• The active site likely adopts a stable, preferred five-coordinate geometry.
• The results suggest the active site is not an imposed entatic state but a naturally stable conformation.