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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.

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.

Schematic diagram showing the role of aromatic dioxygenases in the bacterial degradation of aromatic compounds (Adapted from Khajamohiddin et al., 2008).
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Figure 1: Schematic diagram showing the role of aromatic dioxygenases in the bacterial degradation of aromatic compounds (Adapted from Khajamohiddin et al., 2008).

Mentions: 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. The chemical properties and quantities of the xenobiotic compounds determine their toxicity and persistence in the environment. Organic (aromatic/non-aromatic) compounds constitute a major group of environmental pollutants [1]. These compounds are highly persistent in the environment due to their thermodynamic stability [2]. Many of these compounds have been reported to be toxic to the living organisms [3]. Increased public awareness about the hazards and toxicity of these compounds has encouraged the development of technologies for their remediation. Bioremediation, which utilizes the microbial metabolic potential of the degrading microorganisms, has come up as an efficient and cost-effective means of large scale removal of these compounds in comparison to the physico-chemical means of bioremediation. A number of bacteria that can degrade a variety of aromatic compounds have been identified and the pathways involved in the degradation have been extensively characterized [3,4]. Based on the complexity of the degradation pathways, the phenomenon of biodegradation is categorized into two types: convergent and divergent modes of degradation (Fig. 1). In the convergent mode, structurally diverse aromatic compounds are converted to one of a few aromatic ring cleavage substrates such as catechol, gent sate, protocatechuate and their derivatives [5]. Peripheral enzymes, particularly oxygenases and dehydrogenases, were found to transform structurally diverse substrates into one of these central intermediates by bringing about the hydroxylation of the aromatic nucleus (Fig. 2A), and hence it is thought that bacteria have developed these enzymes to extend their substrate range [5]. There are a number of benefits of channeling diverse compounds into a few central aromatic ring cleavage substrates; the foremost among these being reduction of genetic load and simplification of regulatory circuits. Further, the centralized degradation pathways mean synthesis of fewer degradative enzymes requiring less metabolic energy. This is clearly a major advantage to soil microbes which often find themselves in unfavorable environments containing low concentrations of carbon sources suitable for growth [6]. However, further conversion of these intermediates into tricarboxylic acid (TCA) cycle intermediates was found to be highly diverged (divergent mode) (Fig. 1). In this divergent mode, a metal-dependent dioxygenase channels these dihydroxylated intermediates into one of the two possible pathways: the meta-cleavage pathway or the ortho-cleavage pathway [7-9] (Fig. 1). The substrate specificity of these metal-dependent dioxygenases has been found to play a key role in the overall determination of pathway selection [5] and the dioxygenases have been grouped into two classes namely extradiol and intradiol dioxygenases [7]. Extradiol dioxygenases have nonheme iron (II) at their active site and catalyze ring cleavage at the carbon-carbon (C-C) bond adjacent to the vicinal hydroxyl groups (meta-cleavage) (Fig. 2B) whereas intradiol dioxygenases have non-heme iron (III) in their active site and catalyze ring cleavage at the C-C bond between the vicinal hydroxyl groups (ortho-cleavage) (Fig. 2C). Extradiol dioxygenases channel substrates into a meta-pathway whereas intradiol dioxygenases channel these substrates into an ortho-pathway. Similarly, monoxygenases catalyze the transfer of one atom of molecular oxygen to the organic compound with other being reduced by electrons from cofactors to yield water thereby increasing their reactivity and water solubility.

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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)

Schematic diagram showing the role of aromatic dioxygenases in the bacterial degradation of aromatic compounds (Adapted from Khajamohiddin et al., 2008).
© Copyright Policy - open-access
Figure 1: Schematic diagram showing the role of aromatic dioxygenases in the bacterial degradation of aromatic compounds (Adapted from Khajamohiddin et al., 2008).
Mentions: 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. The chemical properties and quantities of the xenobiotic compounds determine their toxicity and persistence in the environment. Organic (aromatic/non-aromatic) compounds constitute a major group of environmental pollutants [1]. These compounds are highly persistent in the environment due to their thermodynamic stability [2]. Many of these compounds have been reported to be toxic to the living organisms [3]. Increased public awareness about the hazards and toxicity of these compounds has encouraged the development of technologies for their remediation. Bioremediation, which utilizes the microbial metabolic potential of the degrading microorganisms, has come up as an efficient and cost-effective means of large scale removal of these compounds in comparison to the physico-chemical means of bioremediation. A number of bacteria that can degrade a variety of aromatic compounds have been identified and the pathways involved in the degradation have been extensively characterized [3,4]. Based on the complexity of the degradation pathways, the phenomenon of biodegradation is categorized into two types: convergent and divergent modes of degradation (Fig. 1). In the convergent mode, structurally diverse aromatic compounds are converted to one of a few aromatic ring cleavage substrates such as catechol, gent sate, protocatechuate and their derivatives [5]. Peripheral enzymes, particularly oxygenases and dehydrogenases, were found to transform structurally diverse substrates into one of these central intermediates by bringing about the hydroxylation of the aromatic nucleus (Fig. 2A), and hence it is thought that bacteria have developed these enzymes to extend their substrate range [5]. There are a number of benefits of channeling diverse compounds into a few central aromatic ring cleavage substrates; the foremost among these being reduction of genetic load and simplification of regulatory circuits. Further, the centralized degradation pathways mean synthesis of fewer degradative enzymes requiring less metabolic energy. This is clearly a major advantage to soil microbes which often find themselves in unfavorable environments containing low concentrations of carbon sources suitable for growth [6]. However, further conversion of these intermediates into tricarboxylic acid (TCA) cycle intermediates was found to be highly diverged (divergent mode) (Fig. 1). In this divergent mode, a metal-dependent dioxygenase channels these dihydroxylated intermediates into one of the two possible pathways: the meta-cleavage pathway or the ortho-cleavage pathway [7-9] (Fig. 1). The substrate specificity of these metal-dependent dioxygenases has been found to play a key role in the overall determination of pathway selection [5] and the dioxygenases have been grouped into two classes namely extradiol and intradiol dioxygenases [7]. Extradiol dioxygenases have nonheme iron (II) at their active site and catalyze ring cleavage at the carbon-carbon (C-C) bond adjacent to the vicinal hydroxyl groups (meta-cleavage) (Fig. 2B) whereas intradiol dioxygenases have non-heme iron (III) in their active site and catalyze ring cleavage at the C-C bond between the vicinal hydroxyl groups (ortho-cleavage) (Fig. 2C). Extradiol dioxygenases channel substrates into a meta-pathway whereas intradiol dioxygenases channel these substrates into an ortho-pathway. Similarly, monoxygenases catalyze the transfer of one atom of molecular oxygen to the organic compound with other being reduced by electrons from cofactors to yield water thereby increasing their reactivity and water solubility.

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.

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.

View Similar Images In: Results  - Collection
View Article: PubMed Central - HTML -  PubMed
Show All Figures - Show MeSH
getmorefigures.php?pmc=2683861&rFormat=json&query=null&req=5