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MetaCyc Enzyme: nitroarene dioxygenase complex

Species: Comamonas sp. JS765

Subunit composition of nitroarene dioxygenase complex = [NbzAa][NbzAb][(NbzAc)3(NbzAd)3]
         nitroarene dioxygenase complex ferredoxin reductase component = NbzAa
         nitroarene dioxygenase complex ferredoxin component = NbzAb
         nitroarene dioxygenase complex oxygenase component = (NbzAc)3(NbzAd)3
                 nitroarene dioxygenase complex oxygenase component α subunit = NbzAc
                 nitroarene dioxygenase complex oxygenase component β subunit = NbzAd

Summary:
Comamonas sp. JS765 can grow with nitrobenzene as the sole source of carbon, nitrogen, and energy. A key enzyme in this pathway is the nitroarene dioxygenase complex (NBDO), which catalyzes the first step in the degradation of nitrobenzene by strain JS765.

NBDO consists of three components: a ferredoxin reductase component, a ferredoxin component (encoded by the nbzAa and nbzAb genes, respectively) and an oxygenase component. The oxygenase component is a hexamer composed of three subunits each of an α subunit and a β subunit, encoded by the genes nbzAc, and nbzAd, respectively [Parales05].

Sequence analysis showed that the components of NBDO have a high level of homology with the naphthalene family of Rieske nonheme iron oxygenases, and in particular to the 2-nitrotoluene dioxygenase complex from Acidovorax sp. JS42. The enzyme oxidizes a wide range of substrates, and relative reaction rates with partially purified oxygenaseNBZ revealed a preference for 3-nitrotoluene, which is a growth substrate for strain JS765 [Lessner02].

Gene-Reaction Schematic

Gene-Reaction Schematic

Credits:
Created 02-Dec-2004 by Caspi R, SRI International


Enzymatic reaction of: 2-chloro-6-nitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

2-chloro-6-nitrotoluene + NADH + oxygen ⇄ 4-chloro-3-methylcatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 2-chloro-4-nitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

2-chloro-4-nitrotoluene + NADH + oxygen ⇄ 3-chloro-4-methylcatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 1,4-dinitrobenzene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

1,4-dinitrobenzene + NADH + oxygen ⇄ 4-nitrocatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 1,3-dinitrobenzene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

1,3-dinitrobenzene + NADH + oxygen ⇄ 4-nitrocatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 3,4-dinitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

3,4-dinitrotoluene + NADH + oxygen ⇄ 4-methyl-6-nitrocatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 2,6-dinitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

2,6-dinitrotoluene + NADH + oxygen → 3-methyl-4-nitrocatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 4-nitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

4-nitrotoluene + NADH + oxygen ⇄ 4-methylcatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 2-nitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

2-nitrotoluene + NADH + oxygen → 3-methylcatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 2,4-dinitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

2,4-dinitrotoluene + NADH + oxygen ⇄ 4-methyl-3-nitrocatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 2,3-dinitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

2,3-dinitrotoluene + NADH + oxygen ⇄ 4-methyl-3-nitrocatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: 3-nitrotoluene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.23

3-nitrotoluene + NADH + oxygen → 4-methylcatechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
The enzyme could oxidize 3-nitrotoluene with relative activity of 221% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: naphthalene 1,2-dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

EC Number: 1.14.12.12

naphthalene + NADH + H+ + oxygen → cis naphthalene dihydrodiol + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
The enzyme could oxidize naphthalene with relative activity of 59% compared with its nitrobenzene dioxygenase activity [Lessner02].

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Enzymatic reaction of: nitrobenzene dioxygenase (nitroarene dioxygenase complex)

Inferred from experiment

Synonyms: nitrobenzene 1,2-dioxygenase, NBDO

EC Number: 1.14.12.23

nitrobenzene + NADH + oxygen → catechol + nitrite + NAD+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is irreversible in the direction shown.

Alternative Substrates for nitrobenzene: naphthalene [Parales05 ], 1,3-dinitrobenzene [Parales05 ], 4-nitrotoluene [Parales05 ], 3-nitrotoluene [Parales05 ], 2-nitrotoluene [Parales05 ]

In Pathways: nitrobenzene degradation II

Cofactors or Prosthetic Groups: a Rieske [2Fe-2S] iron-sulfur cluster [Parales05], FAD [Parales05]


Subunit of nitroarene dioxygenase complex: nitroarene dioxygenase complex ferredoxin reductase component

Synonyms: reductaseNBZ

Gene: nbzAa Accession Number: G-3921 (MetaCyc)

MultiFun Terms: metabolismcarbon utilizationcarbon compounds


Subunit of nitroarene dioxygenase complex: nitroarene dioxygenase complex ferredoxin component

Synonyms: ferredoxinNBZ

Gene: nbzAb Accession Number: G-3922 (MetaCyc)

Molecular Weight: 14.762 kD (from nucleotide sequence)

Molecular Weight: 11.5 kD (experimental) [Parales05]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Unification Links: Protein Model Portal:Q8RTL5, UniProt:Q8RTL5

Relationship Links: InterPro:IN-FAMILY:IPR017941, Pfam:IN-FAMILY:PF00355, Prosite:IN-FAMILY:PS51296


Subunit of nitroarene dioxygenase complex: nitroarene dioxygenase complex oxygenase component

Synonyms: oxygenaseNBZ

Molecular Weight: 215.9 kD (experimental) [Parales05]


Subunit of nitroarene dioxygenase complex oxygenase component: nitroarene dioxygenase complex oxygenase component α subunit

Synonyms: oxygenaseNBZα

Gene: nbzAc Accession Number: G-3923 (MetaCyc)

Molecular Weight: 49.557 kD (from nucleotide sequence)

Molecular Weight: 51.2 kD (experimental) [Parales05]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Unification Links: DIP:DIP-45324N, Protein Model Portal:Q8RTL4, SMR:Q8RTL4, UniProt:Q8RTL4

Relationship Links: InterPro:IN-FAMILY:IPR001663, InterPro:IN-FAMILY:IPR015879, InterPro:IN-FAMILY:IPR015881, InterPro:IN-FAMILY:IPR017941, PDB:Structure:2BMO, PDB:Structure:2BMQ, PDB:Structure:2BMR, Pfam:IN-FAMILY:PF00355, Pfam:IN-FAMILY:PF00848, Prints:IN-FAMILY:PR00090, Prosite:IN-FAMILY:PS00570, Prosite:IN-FAMILY:PS51296


Subunit of nitroarene dioxygenase complex oxygenase component: nitroarene dioxygenase complex oxygenase component β subunit

Synonyms: oxygenaseNBZβ

Gene: nbzAd Accession Number: G-3924 (MetaCyc)

Molecular Weight: 23.086 kD (from nucleotide sequence)

Molecular Weight: 25.3 kD (experimental) [Parales05]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Unification Links: DIP:DIP-45325N, Protein Model Portal:Q8RTL3, SMR:Q8RTL3, UniProt:Q8RTL3

Relationship Links: InterPro:IN-FAMILY:IPR000391, PDB:Structure:2BMO, PDB:Structure:2BMQ, PDB:Structure:2BMR, Pfam:IN-FAMILY:PF00866


References

Lessner02: Lessner DJ, Johnson GR, Parales RE, Spain JC, Gibson DT (2002). "Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765." Appl Environ Microbiol 68(2);634-41. PMID: 11823201

Parales05: Parales RE, Huang R, Yu CL, Parales JV, Lee FK, Lessner DJ, Ivkovic-Jensen MM, Liu W, Friemann R, Ramaswamy S, Gibson DT (2005). "Purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems." Appl Environ Microbiol 71(7);3806-14. PMID: 16000792

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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