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OxDBase: a database of oxygenases involved in biodegradation.

Arora PK, Kumar M, Chauhan A, Raghava GP, Jain RK - BMC Res Notes (2009)

Bottom Line: Oxygenases belong to the oxidoreductive group of enzymes (E.C.At present the database contains information of over 235 oxygenases including both dioxygenases and monooxygenases.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Environmental Biotechnology, Institute of Microbial Technology, Sector 39-A, Chandigarh-160036, India. parora@imtech.res.in

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/.

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.

No MeSH data available.


Related in: MedlinePlus

Potential uses of oxygenases.
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Figure 5: Potential uses of oxygenases.

Mentions: OxDBase is a knowledge based database that provides comprehensive information about oxygenases including both monooxygenases and dioxygenases. The mechanism of action of the oxygenases is based on hydroxylation of the target molecule. During the recent years, selective hydroxylation of aromatic ring has gained attention in the synthetic biology because of the use of hydroxylated aromatics as drug intermediates. For example, the large scale industrial production of carticosterone, cis-cis muconic acid, pravastatin, indigo and 4-hydroxyproline have been achieved by hydroxylation mechanism of oxygenases [13]. Therefore, the information provided by OxDBase, particularly reaction catalyzed by oxygenases would be a very useful tool for synthesis of various biologically active compounds. OxDBase also provides information of the genes and three dimensional structure of the oxygenases which can help in site directed mutagenesis of the enzymes to improve their catalytic properties. The entries of the oxygenases in OxDBase are linked to various existing database to provide detailed information of oxygenases. Since oxygenases-catalyzed biotransformations of the toxic xenobiotic compounds help in reducing the toxicity of the xenobiotics, therefore, detailed information of these oxygenases would increase our understanding of biodegradation process. The potential uses of these oxygenases have been shown in fig. 5. We hope the OxDBase would be very useful tool for development of better bioremediation strategies as well as synthesis of biologically active compounds.


OxDBase: a database of oxygenases involved in biodegradation.

Arora PK, Kumar M, Chauhan A, Raghava GP, Jain RK - BMC Res Notes (2009)

Potential uses of oxygenases.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2683861&req=5

Figure 5: Potential uses of oxygenases.
Mentions: OxDBase is a knowledge based database that provides comprehensive information about oxygenases including both monooxygenases and dioxygenases. The mechanism of action of the oxygenases is based on hydroxylation of the target molecule. During the recent years, selective hydroxylation of aromatic ring has gained attention in the synthetic biology because of the use of hydroxylated aromatics as drug intermediates. For example, the large scale industrial production of carticosterone, cis-cis muconic acid, pravastatin, indigo and 4-hydroxyproline have been achieved by hydroxylation mechanism of oxygenases [13]. Therefore, the information provided by OxDBase, particularly reaction catalyzed by oxygenases would be a very useful tool for synthesis of various biologically active compounds. OxDBase also provides information of the genes and three dimensional structure of the oxygenases which can help in site directed mutagenesis of the enzymes to improve their catalytic properties. The entries of the oxygenases in OxDBase are linked to various existing database to provide detailed information of oxygenases. Since oxygenases-catalyzed biotransformations of the toxic xenobiotic compounds help in reducing the toxicity of the xenobiotics, therefore, detailed information of these oxygenases would increase our understanding of biodegradation process. The potential uses of these oxygenases have been shown in fig. 5. We hope the OxDBase would be very useful tool for development of better bioremediation strategies as well as synthesis of biologically active compounds.

Bottom Line: Oxygenases belong to the oxidoreductive group of enzymes (E.C.At present the database contains information of over 235 oxygenases including both dioxygenases and monooxygenases.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Environmental Biotechnology, Institute of Microbial Technology, Sector 39-A, Chandigarh-160036, India. parora@imtech.res.in

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/.

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.

No MeSH data available.


Related in: MedlinePlus