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Open Access Data Note

OxDBase: a database of oxygenases involved in biodegradation

Pankaj K Arora1, Manish Kumar2, Archana Chauhan1, Gajendra PS Raghava2 and Rakesh K Jain1*

Author Affiliations

1 Environmental Biotechnology, Institute of Microbial Technology, Sector 39-A, Chandigarh-160036, India

2 Bioinformatics Centre, Institute of Microbial Technology, Sector 39-A, Chandigarh-160036, India

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BMC Research Notes 2009, 2:67  doi:10.1186/1756-0500-2-67

Published: 30 April 2009

Abstract

Background

Oxygenases 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.

Findings

We 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 http://www.imtech.res.in/raghava/oxdbase/ webcite.

Conclusion

OxDBase 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.