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Information on EC 1.14.12.12 - naphthalene 1,2-dioxygenase and Organism(s) Pseudomonas putida and UniProt Accession P0A110

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IUBMB Comments
This enzyme is a member of the ring-hydroxylating dioxygenase (RHD) family of bacterial enzymes that play a critical role in the degradation of aromatic compounds, such as polycyclic aromatic hydrocarbons . This enzyme comprises a multicomponent system, containing a reductase that is an iron-sulfur flavoprotein (FAD; EC 1.18.1.3, ferredoxin---NAD+ reductase), an iron-sulfur oxygenase, and ferredoxin. Requires Fe2+.
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This record set is specific for:
Pseudomonas putida
UNIPROT: P0A110
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Word Map
The taxonomic range for the selected organisms is: Pseudomonas putida
The enzyme appears in selected viruses and cellular organisms
Synonyms
naphthalene dioxygenase, nahac, naphthalene 1,2-dioxygenase, naphthalene oxygenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
naphthalene 1,2-dioxygenase
-
-
naphthalene dioxygenase
naphthalene oxygenase
-
-
-
-
oxygenase, naphthalene di-
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
proposed mechanism
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
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oxidation
-
-
-
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reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
naphthalene,NADH:oxygen oxidoreductase (1,2-hydroxylating)
This enzyme is a member of the ring-hydroxylating dioxygenase (RHD) family of bacterial enzymes that play a critical role in the degradation of aromatic compounds, such as polycyclic aromatic hydrocarbons [5]. This enzyme comprises a multicomponent system, containing a reductase that is an iron-sulfur flavoprotein (FAD; EC 1.18.1.3, ferredoxin---NAD+ reductase), an iron-sulfur oxygenase, and ferredoxin. Requires Fe2+.
CAS REGISTRY NUMBER
COMMENTARY hide
9074-04-8
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
acenaphthene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
acenaphthylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
anthanthrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
anthracene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[a]coronene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[a]naphthacene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[a]pyrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[b]chrysene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[b]fluorene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[c]chrysene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[c]phenanthrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[e]pyrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[ghi]fluoranthene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[ghi]naphtho[cde]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[ghi]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[j]fluoranthene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[rst]dinaphtho[defg,ijkl]pentaphene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benzo[rst]phenanthro[1,10,9-cde]pentaphene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benz[a]anthracene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benz[e]acephenanthrylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
benz[rst]anthra[cde]pentaphene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
chrysene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
coronene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenzo[b,def]chrysene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenzo[bc,ef]coronene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenzo[g,p]chrysene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenzo[j,lm]naphtho[ab]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenz[a,c]anthracene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenz[a,h]anthracene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dibenz[a,j]anthracene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
dinaphtho[defg,opqr]pentacene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
fluoranthene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
fluorine + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
hexabenzo[a,cd,f,j,lm,o]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
naphthacene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
naphthalene + NADH + H+ + O2
(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
naphtho[a]anthracene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
naphtho[bcd]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
naphtho[d]coronene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
pentabenzo[a,cd,f,j,lm]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
pentacene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
pentaphene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
phenanthrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
phenanthro[3,4-c]phenanthrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
picene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
pyranthrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
pyrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
tetrabenzo[a,cd,f,lm]perylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
triphenylene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
?
1,3-benzodithiole + NADH + O2
(R)-1,3-benzodithiole-1-oxide + NAD+
show the reaction diagram
-
-
-
-
?
1,4-benzo[d]dithiine + NADH + O2
(S)-1,4-benzo[d]dithiin-1-oxide + NAD+
show the reaction diagram
-
-
-
-
?
2,3-dihydro-1,4-benzo[d]dithiine + NADH + O2
(S)-2,3-dihydrobenzo[d]dithiin-1-oxide + NAD+
show the reaction diagram
-
-
-
-
?
2-chlorobiphenyl + NADH + O2
2-chloro-2',3'-dihydrobiphenyl-2',3'-diol + NAD+
show the reaction diagram
-
recombinant histidine-tagged terminal dioxygenase
-
?
2-methyl-1,3-benzodithiole + NADH + O2
(1S,2R)-2-methyl-1,3-benzodithiole-1-oxide + (1S,2S)-2-methyl-1,3-benzodithiole-1-oxide + NAD+
show the reaction diagram
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-
cis and trans product
-
?
3,4-dihydro-2H-1lambda4,5-benzodithiepin + NADH + O2
(S)-1,2,3,4-tetrahydro-1lambda4,5-benzodithiepin-1-oxide + NAD+
show the reaction diagram
-
-
-
-
?
3-chlorobiphenyl + NADH + O2
3-chloro-2',3'-dihydrobiphenyl-2',3'-diol + NAD+
show the reaction diagram
-
recombinant histidine-tagged terminal dioxygenase
-
?
4-chlorobiphenyl + NADH + O2
4-chloro-2',3'-dihydrobiphenyl-2',3'-diol + NAD+
show the reaction diagram
-
recombinant histidine-tagged terminal dioxygenase
-
?
benzpyrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
-
?
fulvic acid + NADH + H+ + O2
?
show the reaction diagram
-
-
-
-
?
humic acid + NADH + H+ + O2
?
show the reaction diagram
-
-
-
-
?
indan + NADH + H+ + O2
1-indanol + NAD+
show the reaction diagram
-
-
-
?
indole + ? + O2
cis-indole-2,3-dihydrodiol
show the reaction diagram
-
reaction of recombinant E. coli transformed with Pseudomonas sp. DNA
-
?
indole + NADH + H+ + O2
?
show the reaction diagram
-
-
-
-
?
naphthalene + NAD(P)H + O2
cis-(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD(P)+
show the reaction diagram
-
-
only cis-isomer by bacteria, product rapidly autooxidizes to 1,2-naphthoquinone
?
naphthalene + NADH + H+ + O2
(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
naphthalene + NADH + H+ + O2
1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
-
-
-
-
?
naphthalene + NADH + O2
(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
-
initial oxidative reaction in bacterial naphthalene catabolism
-
?
phenanthrene + NADH + H+ + O2
?
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
naphthalene + NADH + H+ + O2
(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
naphthalene + NADH + H+ + O2
(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
naphthalene + NADH + O2
(1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
show the reaction diagram
-
initial oxidative reaction in bacterial naphthalene catabolism
-
?
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
-
the naphthalene dioxygenase system can develop the capacity of plants to tolerate a high concentration of phenanthrene and metabolize phenanthrene in vivo
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NDOB_PSEPU
449
0
49608
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
-
x * 53000 + x * 25000, histidine-tagged recombinant enzyme, SDS-PAGE
53000
-
x * 53000 + x * 25000, histidine-tagged recombinant enzyme, SDS-PAGE
additional information
-
three component enzyme system consisting of: component A, i.e. ferredoxinNAP reductase, component B, i.e. terminal oxygenase ISPNAP, and component C, i.e. ferredoxinNAP
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 53000 + x * 25000, histidine-tagged recombinant enzyme, SDS-PAGE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
23-25°C, buffer, 14 days, loss of about 80% activity
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
metal affinity chromatography
-
Ni-NTA column chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli, Arabidopsis thaliana and Oryza sativa
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expression of histidine tagged enzyme in Escherichia coli
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His-tagged, expressed in Escherichia coli
-
strain G7, fragment of plasmid NAH7 cloned and expressed in Escherichia coli HB101
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Jeffrey, A.M.; Yeh, H.J.C.; Jerina, D.M.; Patel, T.R.; Davey, J.F.; Gibson, D.T.
Initial reactions in the oxidation of naphthalene by Pseudomonas putida
Biochemistry
14
575-584
1975
Pseudomonas putida, Pseudomonas putida 119
Manually annotated by BRENDA team
Ensley, B.D.; Ratzkin, B.J.; Osslund, T.D.; Simon, M.J.; Wackett, L.P.; Gibson, D.T.
Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo
Science
222
167-169
1983
Pseudomonas putida, Pseudomonas putida G7
Manually annotated by BRENDA team
Barriault, D.; Sylvestre, M.
Functionality of biphenyl 2,3-dioxygenase components in naphthalene 1,2-dioxygenase
Appl. Microbiol. Biotechnol.
51
592-597
1999
Pseudomonas putida, Pseudomonas putida G7
Manually annotated by BRENDA team
Wackett, L.P.; Kwart, L.D.; Gibson, D.T.
Benzylic monooxygenation catalyzed by toluene dioxygenase from Pseudomonas putida
Biochemistry
27
1360-1367
1988
Pseudomonas putida
Manually annotated by BRENDA team
Boyd, D.R.; Sharma, N.D.; Haughey, S.A.; Kennedy, M.A.; Malone, J.F.; Shepherd, S.D.; Allen, C.C.R.; Dalton, H.
Dioxygenase-catalyzed sulfoxidation of bicyclic alkylaryl sulfides and chemoenzymatic synthesis of acyclic disulfoxides
Tetrahedron
60
549-559
2004
Pseudomonas putida, Pseudomonas putida 8859
-
Manually annotated by BRENDA team
Piskonen, R.; Nyyssoenen, M.; Itaevaara, M.
Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes
Biodegradation
19
883-895
2008
Pseudomonas putida (P0A110 and P0A112), Pseudomonas putida, Pseudomonas putida G7 (P0A110 and P0A112)
Manually annotated by BRENDA team
AbuBakr, S.; Macmil, S.; Nanny, M.; Duncan, K.
Enzymatic transformation of humic substances by NDO
Soil Biol. Biochem.
40
2055-2062
2008
Pseudomonas putida, Pseudomonas putida G7
Manually annotated by BRENDA team
Dutta, K.; Shityakov, S.; Das, P.P.; Ghosh, C.
Enhanced biodegradation of mixed PAHs by mutated naphthalene 1,2-dioxygenase encoded by Pseudomonas putida strain KD6 isolated from petroleum refinery waste
3 Biotech
7
365
2017
Pseudomonas putida, Pseudomonas putida KD6
Manually annotated by BRENDA team
Peng, R.H.; Fu, X.Y.; Zhao, W.; Tian, Y.S.; Zhu, B.; Han, H.J.; Xu, J.; Yao, Q.H.
Phytoremediation of phenanthrene by transgenic plants transformed with a naphthalene dioxygenase system from Pseudomonas
Environ. Sci. Technol.
48
12824-12832
2014
Pseudomonas putida
Manually annotated by BRENDA team
Escalante, D.E.; Aukema, K.G.; Wackett, L.P.; Aksan, A.
Simulation of the bottleneck controlling access into a Rieske active site Predicting substrates of naphthalene 1,2-dioxygenase
J. Chem. Inf. Model.
57
550-561
2017
Pseudomonas putida (P0A110), Pseudomonas putida (P0A112)
Manually annotated by BRENDA team
Librando, V.; Pappalardo, M.
Theoretical approach to the innovative mutation of naphthalene 1,2-dioxygenase a molecular dynamics and docking study
J. Mol. Model.
20
2354
2014
Pseudomonas putida (P0A110)
Manually annotated by BRENDA team