OxDBase: a database of oxygenases involved in biodegradation

Area of Science:

• Biochemistry
• Enzymology
• Bioinformatics

Background:

• Oxygenases are oxidoreductive enzymes (E.C. Class 1) that utilize molecular oxygen and co-substrates like FAD/NADH/NADPH.
• These enzymes are crucial for organic compound metabolism, enhancing reactivity, water solubility, or aromatic ring cleavage.
• Oxygenases are classified as monooxygenases or dioxygenases based on oxygen atom utilization.

Purpose of the Study:

• To create a comprehensive, web-accessible database of biodegradative oxygenases.
• To consolidate information from primary literature into a searchable resource.
• To facilitate research in synthetic chemistry and bioremediation.

Main Methods:

• Compiled data from primary literature on oxygenases.
• Developed a web-accessible database named OxDBase.
• Implemented separate search engines for monooxygenases and dioxygenases.
• Integrated links to external databases (BRENDA, KEGG, ENZYME, UM-BBD) for extended information.

Main Results:

• OxDBase contains information on over 235 oxygenases, including both monooxygenases and dioxygenases.
• Each entry includes enzyme name, synonyms, reactions, family, subfamily, structure, gene links, and literature citations.
• The database is freely available online at http://www.imtech.res.in/raghava/oxdbase/.

Conclusions:

• OxDBase is the first dedicated database for oxygenases, offering comprehensive data.
• The database is a valuable tool for synthetic chemistry, particularly in drug intermediate synthesis.
• OxDBase supports bioremediation efforts through its detailed information on xenobiotic compound oxidation.