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The catalytic cycle of catechol oxidase
1Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden. ps@physto.se
Summary
This study reveals the catalytic mechanism of catechol oxidase, a copper-containing enzyme. The key step involves peroxide O-O bond cleavage coupled with proton transfer, aligning with experimental data.
Area of Science:
- Biochemistry
- Computational Chemistry
- Enzymology
Background:
- Catechol oxidase is a copper-containing enzyme with a dimeric active site coordinated by histidine ligands.
- It shares structural and functional similarities with tyrosinase, another enzyme in this class.
- The availability of X-ray crystal structures for catechol oxidase facilitates detailed mechanistic investigations.
Purpose of the Study:
- To elucidate the catalytic mechanism of catechol oxidase using computational methods.
- To identify the rate-determining step and key intermediates in the enzymatic reaction.
- To compare the mechanism with that of related enzymes like tyrosinase.
Main Methods:
- Hybrid density functional theory (DFT) calculations employing the B3LYP functional.
- Investigation of the active site structure and catalytic cycle of catechol oxidase.
- Analysis of transition states and reaction energetics.
Main Results:
- The critical step involves the cleavage of the peroxide O-O bond, occurring concurrently with substrate proton transfer.
- A subsequent proton transfer from the substrate completes water molecule formation.
- The mechanism does not require proton exchange with amino acid residues outside the copper-binding site.
Conclusions:
- The proposed mechanism for catechol oxidase is supported by calculated energetics that agree well with experimental observations.
- The findings provide insights into the structure-function relationship of copper-containing enzymes.
- This study contributes to understanding enzymatic catalysis and can inform the design of bio-inspired catalysts.