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Information on EC 1.14.12.18 - biphenyl 2,3-dioxygenase and Organism(s) Comamonas testosteroni and UniProt Accession Q46372

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IUBMB Comments
Requires Fe2+. The enzyme from Burkholderia fungorum LB400 (previously Pseudomonas sp.) is part of a multicomponent system composed of an NADH:ferredoxin oxidoreductase (FAD cofactor), a [2Fe-2S] Rieske-type ferredoxin, and a terminal oxygenase that contains a [2Fe-2S] Rieske-type iron-sulfur cluster and a catalytic mononuclear nonheme iron centre. Chlorine-substituted biphenyls can also act as substrates. Similar to the three-component enzyme systems EC 1.14.12.3 (benzene 1,2-dioxygenase) and EC 1.14.12.11 (toluene dioxygenase).
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Comamonas testosteroni
UNIPROT: Q46372
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The taxonomic range for the selected organisms is: Comamonas testosteroni
The enzyme appears in selected viruses and cellular organisms
Synonyms
biphenyl dioxygenase, bpha1, bph dox, biphenyl 2,3-dioxygenase, bphabc, bphae, biphenyl-2,3-dioxygenase, bphabcd, bpdolb400, bpha1a2, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biphenyl dioxygenase
-
biphenyl-2,3-dioxygenase
-
BDO
-
-
-
-
Biphenyl 2,3-dioxygenase
-
-
-
-
biphenyl dioxygenase
BPH dox
-
-
-
-
BPO
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
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oxidation
-
-
-
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reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
biphenyl,NADH:oxygen oxidoreductase (2,3-hydroxylating)
Requires Fe2+. The enzyme from Burkholderia fungorum LB400 (previously Pseudomonas sp.) is part of a multicomponent system composed of an NADH:ferredoxin oxidoreductase (FAD cofactor), a [2Fe-2S] Rieske-type ferredoxin, and a terminal oxygenase that contains a [2Fe-2S] Rieske-type iron-sulfur cluster and a catalytic mononuclear nonheme iron centre. Chlorine-substituted biphenyls can also act as substrates. Similar to the three-component enzyme systems EC 1.14.12.3 (benzene 1,2-dioxygenase) and EC 1.14.12.11 (toluene dioxygenase).
CAS REGISTRY NUMBER
COMMENTARY hide
103289-55-0
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3,3'-dichlorobiphenyl + NADH + H+ + O2
5,6-dihydroxy-1-phenylcyclohexa-1,3-diene + 4,5-dihydroxy-1-phenylcyclohexa-1,2-diene + NAD+ + HCl
show the reaction diagram
-
-
-
?
4,4'-dichlorobiphenyl + NADH + H+ + O2
2,3-dihydroxy-4,4'-dichlorobiphenyl + NAD+
show the reaction diagram
-
-
-
?
biphenyl + NADH + H+ + O2
2,3-dihydro-dihydroxybiphenyl + NAD+
show the reaction diagram
-
-
-
?
2,2',3,3'-tetrachlorobiphenyl + NADH + O2
?
show the reaction diagram
-
-
-
-
?
2,2'-dichlorobiphenyl + NADH + H+ + O2
?
show the reaction diagram
-
wild-type enzyme
-
-
?
2,2'-dichlorobiphenyl + NADH + O2
5,6-dihydroxy-1-phenylcyclohexa-1,3-diene + 2,3-dihydroxy-2'-chlorobiphenyl + NAD+ + HCl
show the reaction diagram
-
-
-
-
?
2,3',4'-trichlorobiphenyl + NADH + O2
?
show the reaction diagram
-
-
-
-
?
2,3,4'-trichlorobiphenyl + NADH + O2
?
show the reaction diagram
-
-
-
-
?
2,5-dichlorobiphenyl + NADH + O2
cis-2',3'-dihydroxy-1'-(2,5-dichlorophenyl)-cyclohexa-4',6'-diene + 3,4-dihydroxy-1-phenylcyclohexa-1,5-diene + NAD+ + HCl
show the reaction diagram
-
no 3,4-dihydrodiol as product
-
-
?
2-hydroxy-3,5-dichlorobiphenyl + NADH + H+ + O2
?
show the reaction diagram
-
ortho-meta-oxygenation, hydroxylation on the non-substituted ring
-
-
?
2-hydroxy-3-chlorobiphenyl + NADH + H+ + O2
5-(3-chloro-2-hydroxyphenyl)-6-hydroxy-3-cyclohexen-1-one + NAD+
show the reaction diagram
-
ortho-meta-oxygenation, hydroxylation on the non-substituted ring
+ minor amounts of dihydroxybiphenyl, generated by the rearrangement of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-3'-chlorobiphenyl and minor amounts of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-3'-chlorobiphenyl and 2-hydroxy-3-chloro-2',3'-dihydroxybiphenyl. 5-(3-chloro-2-hydroxyphenyl)-6-hydroxy-3-cyclohexen-1-one is likely generated from the rearrangement of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-3'-chlorobiphenyl
-
?
2-hydroxy-5-chlorobiphenyl + NADH + H+ + O2
cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-5'-chlorobiphenyl + 5-(5-chloro-2-hydroxyphenyl)-6-hydroxy-3-cyclohexene-1-one + 2,2'-dihydroxy-5-chlorobiphenyl + 2,3'-dihydroxy-5-chlorobiphenyl + NAD+
show the reaction diagram
-
ortho-meta-oxygenation, hydroxylation on the non-substituted ring
minor amounts of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-5'-chlorobiphenyl are also found as well as 2-hydroxy-5-chloro-2',3'-dihydroxybiphenyl which is most likely generated by spontaneous rearrangement and dehydrogenation of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-5'-chlorobiphenyl. 5-(5-chloro-2-hydroxyphenyl)-6-hydroxy-3-cyclohexene-1-oneis likely to be generated from rearrangement of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-5'-chlorobiphenyl. 2,2'-Dihydroxy-5-chlorobiphenyl and 2,3'-dihydroxy-5-chlorobiphenyl are also generated by the loss of OH and rearrangement of cis-2,3-dihydro-2,3-dihydroxy-2'-hydroxy-5'-chlorobiphenyl
-
?
3,3'-dichlorobiphenyl + NADH + H+ + O2
?
show the reaction diagram
-
wild-type enzyme
-
-
?
3,3'-dichlorobiphenyl + NADH + O2
5,6-dihydroxy-1-phenylcyclohexa-1,3-diene + 4,5-dihydroxy-1-phenylcyclohexa-1,2-diene + NAD+ + HCl
show the reaction diagram
-
-
-
-
?
3,3'-dichlorobiphenyl + NADH + O2
?
show the reaction diagram
-
-
-
-
?
biphenyl + NAD(P)H + O2
2,3-dihydro-dihydroxybiphenyl + NAD(P)+
show the reaction diagram
-
-
-
-
?
biphenyl + NADH + H+ + O2
?
show the reaction diagram
-
wild-type enzyme
-
-
?
dibenzo-p-dioxin + NADH + O2
2,2',3-trihydroxybiphenyl ether + NAD+
show the reaction diagram
-
-
-
-
?
dibenzofurane + NADH + O2
2,2',3-trihydroxybiphenyl + dihydro-dihydroxy-dibenzofuran + NAD+
show the reaction diagram
-
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+ small amounts of 2,2',3-trihydroxybiphenyl. 2,2',3-dihydroxybiphenyl results from angular oxygenation, dihydro-dihydroxy-dibenzofuran results from lateral oxygenation
-
?
additional information
?
-
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no activity with 4,4'-dichlorobiphenyl and 2,2',5,5'-tetrachlorobiphenyl
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ferredoxin
-
part of a multicomponent enzyme
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
coordination geometry of Fe-ion along with the oxygen and different polychlorinated biphenyl congeners
Fe2+
-
contains a [2Fe-2S] Rieske-type center carrying a mononuclear Fe2+
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
exposure of soil microcosms to different polychlorinated biphenyl congeners results in different bacterial community structures and abundance of BPH genes
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0026
2,2'-dichlorobiphenyl
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recombinant, purified protein
0.0033
3,3'-dichlorobiphenyl
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recombinant, purified protein
0.0062 - 1.1
biphenyl
0.028
O2
-
recombinant, purified protein
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.9
-
recombinant protein after purification
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
BPHA_COMTE
457
0
51692
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
186000
-
native protein with His-tag, HPLC gel filtration
234000
-
native protein, HPLC gel filtration
25200
-
beta subunit with His-tag, SDS-PAGE
44000
-
native, recombinant and purified alpha subunit with His-tag, HPLC gel filtration
53600
-
alpha subunit with His-tag, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
construction of a three-dimensional model of alpha-subunit of biphenyl dioxygenase (BphA). BphA active site is composed of two domains, the catalytic domain (residues 1-58 and 176-457) and the Rieske domain (residues 59–166). The active site pocket, which is lined mostly by hydrophobic residues (Phe227, Trp390, Phe 376, Asp386, Phe382 and Ala234) is located between the core beta-sheet and alpha-helices in the catalytic domain of the alpha-subunit
?
-
diversity of the C-terminal portion of the biphenyl dioxygenase large subunit
heterohexamer
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alpha3,beta3, 3 * 53600 + 3 * 25200, SDS-PAGE and gel filtration
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
N348H
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wild-type enzyme shows less than 10% activity with 2,6-dichlorobiphenyl, 4,4'-dichlorobiphenyl - mutant enzyme shows about 55% depletion. Wild-type enzyme shows no degradation of 2,4,4'-trichlorobiphenyl and 2,2',5,5'-tetrachlorobiphenyl - mutant enzyme shows 50% and 92% depletion
N348H/A404V
-
wild-type enzyme shows less than 10% activity with 2,6-dichlorobiphenyl, 4,4'-dichlorobiphenyl - mutant enzyme shows about 55% depletion. Wild-type enzyme shows no degradation of 2,4,4'-trichlorobiphenyl and 2,2',5,5'-tetrachlorobiphenyl - mutant enzyme shows 29% and 84% depletion
T375N
-
conversion of sequence to corresponding sequence of Pseudomonas sp. strain LB400
additional information
-
characterization of hybrid biphenyl dioxygenases obtained by recombining Burkholderia sp. strain Comamonas testosteroni LB400 bphA with the homologous gene of Comamonas testosteroni B-356. The C-terminal portion of Burkholderia sp. LB400 alpha-subunit can withstand extensive structural modifications, and that these modifications can change the catalytic properties of the enzyme. Exchanging the C-terminal portion of Comamonas testosteroni B-356 BPDO alpha-subunit with that of Burkholderia sp. LB400 alpha-subunit generates inactive chimeras
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
20 min preincubation of His-tagged enzyme with 5 mM dithiothreitol on ice can restore activity of older preparations
-
285287
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, several months
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
His-tagged ISP, expressed in Escherichia coli
-
purification from heterologous expression in Pseudomonas putida KT2442
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
in Escherichia coli, strains M15 and SG13009
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in Pseudomonas putida strain KT2442
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hurtubise, Y.; Barriault, D.; Sylvestre, M.
Characterization of active recombinant His-tagged oxygenase component of Comamonas testosteroni B-356 biphenyl dioxygenase
J. Biol. Chem.
271
8152-8156
1996
Comamonas testosteroni
Manually annotated by BRENDA team
Hurtubise, Y.; Barriault, D.; Sylvestre, M.
Involvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls
J. Bacteriol.
180
5828-5835
1998
Comamonas testosteroni, Pseudomonas sp., Pseudomonas sp. LB400
Manually annotated by BRENDA team
Imbeault, N.Y.; Powlowski, J.B.; Colbert, C.L.; Bolin, J.T.; Eltis, L.D.
Steady-state kinetic characterization and crystallization of a polychlorinated biphenyl-transforming dioxygenase
J. Biol. Chem.
275
12430-12437
2000
Comamonas testosteroni
Manually annotated by BRENDA team
L'Abbee J.B.; Barriault, D.; Sylvestre, M.
Metabolism of dibenzofuran and dibenzo-p-dioxin by the biphenyl dioxygenase of Burkholderia xenovorans LB400 and Comamonas testosteroni B-356
Appl. Microbiol. Biotechnol.
67
506-514
2005
Comamonas testosteroni, Paraburkholderia xenovorans
Manually annotated by BRENDA team
Barriault, D.; Simard, C.; Chatel, H.; Sylvestre, M.
Characterization of hybrid biphenyl dioxygenases obtained by recombining Burkholderia sp. strain LB400 bphA with the homologous gene of Comamonas testosteroni B-356
Can. J. Microbiol.
47
1025-1032
2001
Burkholderia sp., Comamonas testosteroni
Manually annotated by BRENDA team
Francova, K.; Mackova, M.; Macek, T.; Sylvestre, M.
Ability of bacterial biphenyl dioxygenases from Burkholderia sp. LB400 and Comamonas testosteroni B-356 to catalyse oxygenation of ortho-hydroxychlorobiphenyls formed from PCBs by plants
Environ. Pollut.
127
41-48
2004
Burkholderia sp., Burkholderia sp. LB400, Comamonas testosteroni
Manually annotated by BRENDA team
Barriault, D.; Plante, M.M.; Sylvestre, M.
Family shuffling of a targeted bphA region to engineer biphenyl dioxygenase
J. Bacteriol.
184
3794-3800
2002
Burkholderia sp., Comamonas testosteroni, Burkholderia sp. LB4000
Manually annotated by BRENDA team
Witzig, R.; Junca, H.; Hecht, H.J.; Pieper, D.H.
Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases
Appl. Environ. Microbiol.
72
3504-3514
2006
Pseudomonas aeruginosa, Burkholderia sp. (O86136), Paraburkholderia xenovorans (P37333), Comamonas testosteroni (Q46372), Comamonas testosteroni (Q8KZP9), Pseudomonas oleovorans (Q52028), Pseudomonas sp. (Q52438), Rhodococcus globerulus (Q52757), Rhodococcus sp. (Q53122), Rhodococcus erythropolis (Q79EP8), Pseudomonas aeruginosa JI104, Rhodococcus globerulus P6 (Q52757), Pseudomonas oleovorans KF707 (Q52028), Rhodococcus erythropolis TA421 (Q79EP8)
Manually annotated by BRENDA team
Correa, P.A.; Lin, L.; Just, C.L.; Hu, D.; Hornbuckle, K.C.; Schnoor, J.L.; Van Aken, B.
The effects of individual PCB congeners on the soil bacterial community structure and the abundance of biphenyl dioxygenase genes
Environ. Int.
36
906-910
2010
Burkholderia sp. JB1, Comamonas testosteroni, Paraburkholderia xenovorans LB400, Pseudomonas oleovorans, Pseudomonas oleovorans KF707, Pseudomonas sp. B4, Rhodococcus erythropolis, Rhodococcus erythropolis TA421, Rhodococcus globerulus, Rhodococcus globerulus P6
Manually annotated by BRENDA team
Baig, M.S.; Manickam, N.
Homology modeling and docking studies of Comamonas testosteroni B-356 biphenyl-2,3-dioxygenase involved in degradation of polychlorinated biphenyls
Int. J. Biol. Macromol.
46
47-53
2010
Comamonas testosteroni (Q46372)
Manually annotated by BRENDA team
Vezina, J.; Barriault, D.; Sylvestre, M.
Diversity of the C-terminal portion of the biphenyl dioxygenase large subunit
J. Mol. Microbiol. Biotechnol.
15
139-151
2008
Acidovorax sp. B-206 (A6N2I5), bacterium B-358 (A6N2I7), bacterium YT01 (A6N2I8), Comamonas testosteroni, Comamonas testosteroni TK102, Cupriavidus necator, Cupriavidus necator A5, Cupriavidus necator H850, Paenibacillus sp. B-257 (A6N2I6), Pandoraea pnomenusa, Pandoraea pnomenusa B-356, Paraburkholderia xenovorans LB400, Pseudomonas alcaligenes, Pseudomonas alcaligenes B-357, Pseudomonas oleovorans, Pseudomonas oleovorans KF707, Pseudomonas sp. Cam-1, Pseudomonas sp. JB-1, Pseudomonas sp. KKS102, Rhodococcus globerulus, Rhodococcus globerulus P6, uncultured soil bacterium (A5YWJ0), uncultured soil bacterium (A5YWJ1), uncultured soil bacterium (A5YWJ2), uncultured soil bacterium (A5YWJ3), uncultured soil bacterium (A5YWJ4), uncultured soil bacterium (A5YWJ5), uncultured soil bacterium (A5YWJ6), uncultured soil bacterium (A5YWJ7), uncultured soil bacterium (A5YWJ8), uncultured soil bacterium (A5YWJ9), uncultured soil bacterium (A5YWK0), uncultured soil bacterium (A5YWK1), uncultured soil bacterium (A5YWK2), uncultured soil bacterium (A5YWK3), uncultured soil bacterium (A5YWK4), uncultured soil bacterium (A5YWK5), uncultured soil bacterium (A5YWK6)
Manually annotated by BRENDA team