Abstract
BackgroundOxygenases belong to the oxidoreductive group of enzymes (E.C. Class 1), which oxidize the substrates by transferring oxygen from molecular oxygen (O2) and utilize FAD/NADH/NADPH as the co-substrate. Oxygenases can further be grouped into two categories i.e. monooxygenases and dioxygenases on the basis of number of oxygen atoms used for oxidation. They play a key role in the metabolism of organic compounds by increasing their reactivity or water solubility or bringing about cleavage of the aromatic ring.FindingsWe compiled a database of biodegradative oxygenases (OxDBase) which provides a compilation of the oxygenase data as sourced from primary literature in the form of web accessible database. There are two separate search engines for searching into the database i.e. mono and dioxygenases database respectively. Each enzyme entry contains its common name and synonym, reaction in which enzyme is involved, family and subfamily, structure and gene link and literature citation. The entries are also linked to several external database including BRENDA, KEGG, ENZYME and UM-BBD providing wide background information. At present the database contains information of over 235 oxygenases including both dioxygenases and monooxygenases. This database is freely available online at .ConclusionOxDBase is the first database that is dedicated only to oxygenases and provides comprehensive information about them. Due to the importance of the oxygenases in chemical synthesis of drug intermediates and oxidation of xenobiotic compounds, OxDBase database would be very useful tool in the field of synthetic chemistry as well as bioremediation.
Highlights
Oxygenases belong to the oxidoreductive group of enzymes
In the last few decades, extensive urbanization and rapid industrialization has resulted in the addition of a large number of xenobiotic compounds into the environment
Increased public awareness about the hazards and toxicity of these compounds has encouraged the development of technologies for their
Summary
OxDBase is a unique database which provides comprehensive information about oxygenases. It is a platform from which users can retrieve information on all available oxygenases. The present database would increase our understanding of the biological, biochemical, genomic, evolutionary and structural properties of oxygenases that could be exploited for industrial and bioremediation applications. FAD: Flavin Adenine Dinucleotide; NADH: Nicotinamide Adenine Dinucleotide Reduced; NADP: Nicotinamide Adenine Dinucleotide Phosphate Reduced; PERL: Practical Extraction and Report Language; NCBI: National Center for Biotechnology Information; PDB: Protein Data Bank.; BRENDA: The Comprehensive Enzyme Information System; UM-BBD: University of Minnesota Biocatalysis/Biodegradation Database; IUBMB: International Union of Biochemistry and Molecular Biology; KEGG: Existing Databases. Kyoto Encyclopedia of Genes and Genomes; ENZYME: Enzyme Nomenclature Database
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