Information on EC 1.13.11.39 - biphenyl-2,3-diol 1,2-dioxygenase

New: Word Map on EC 1.13.11.39
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Mark a special word or phrase in this record:
Search Reference ID:
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY hide
1.13.11.39
-
RECOMMENDED NAME
GeneOntology No.
biphenyl-2,3-diol 1,2-dioxygenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
show the reaction diagram
also acts on 3-isopropylcatechol, forming 7-methyl-2-hydroxy-6-oxoocta-2,4-dienoate. Not identical with EC1.13.11.2 catechol 2,3-dioxygenase
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dioxygenation
-
-
-
-
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
2-hydroxybiphenyl degradation
-
-
biphenyl degradation
-
-
carbazole degradation
-
-
Chlorocyclohexane and chlorobenzene degradation
-
-
Dioxin degradation
-
-
diphenyl ethers degradation
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
biphenyl-2,3-diol:oxygen 1,2-oxidoreductase (decyclizing)
Contains Fe2+ or Mn2+ [3]. This enzyme participates in the degradation pathway of biphenyl and PCB (poly chlorinated biphenyls), and catalyses the first ring cleavage step by incorporating two oxygen atoms into the catechol ring formed by EC 1.3.1.56, cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase.The enzyme from the bacterium Burkholderia xenovorans LB400 can also process catechol, 3-methylcatechol, and 4-methylcatechol, but less efficiently [1]. The enzyme from the carbazole-degrader Pseudomonas resinovorans strain CA10 also accepts 2'-aminobiphenyl-2,3-diol [5]. The enzyme from Ralstonia sp. SBUG 290 can also accept 1,2-dihydroxydibenzofuran and 1,2-dihydroxynaphthalene [4]. The enzyme is strongly inhibited by the substrate [1].Not identical with EC 1.13.11.2 catechol 2,3-dioxygenase.
CAS REGISTRY NUMBER
COMMENTARY hide
103679-58-9
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
strain LB400
-
-
Manually annotated by BRENDA team
LB400
-
-
Manually annotated by BRENDA team
LB400
-
-
Manually annotated by BRENDA team
Burkholderia xenovorans
strain LB400
-
-
Manually annotated by BRENDA team
SMN4
-
-
Manually annotated by BRENDA team
SMN4
-
-
Manually annotated by BRENDA team
strain B-356
-
-
Manually annotated by BRENDA team
strain H850
-
-
Manually annotated by BRENDA team
strain H850
-
-
Manually annotated by BRENDA team
strain BCG
-
-
Manually annotated by BRENDA team
strain KF714
-
-
Manually annotated by BRENDA team
strain KF715
-
-
Manually annotated by BRENDA team
strain KT2442
-
-
Manually annotated by BRENDA team
strain OU83, EMBL nucleotide database
SwissProt
Manually annotated by BRENDA team
strain PpG7
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain CB406
-
-
Manually annotated by BRENDA team
strain DJ-12
-
-
Manually annotated by BRENDA team
strain DJ77
-
-
Manually annotated by BRENDA team
strain IC
-
-
Manually annotated by BRENDA team
ATCC 31258
-
-
Manually annotated by BRENDA team
strain SBUG 290
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain SBUG 290
-
-
Manually annotated by BRENDA team
strain TA421
-
-
Manually annotated by BRENDA team
strain TA421
-
-
Manually annotated by BRENDA team
strain RHA1
SwissProt
Manually annotated by BRENDA team
strain Q1
-
-
Manually annotated by BRENDA team
strain BN6
-
-
Manually annotated by BRENDA team
strain BN6
-
-
Manually annotated by BRENDA team
activated sludge metagenome, gene bphC_meta
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,2-dihydroxydibenzofuran + O2
?
show the reaction diagram
-
-
-
-
?
1,2-dihydroxynaphthalene + O2
?
show the reaction diagram
-
-
-
-
?
2',3',5'-trichloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(2',3',5'-trichlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
2',3'-dichloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(2',3'-dichlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
2',4'-dichloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(2',4'-dichlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
2'-aminobiphenyl-2,3-diol + O2
(2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate + H+
show the reaction diagram
2'-aminobiphenyl-2,3-diol + O2
?
show the reaction diagram
-
-
-
-
?
2'-chloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(2'-chlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
2,2',3,3'-tetrachlorobiphenyl + O2
?
show the reaction diagram
Burkholderia xenovorans
-
-
-
-
?
2,2',3-trihydroxybiphenyl + O2
?
show the reaction diagram
-
-
-
-
?
2,2'-dibromobiphenyl + O2
?
show the reaction diagram
2,2'-dichlorobiphenyl + O2
?
show the reaction diagram
2,2'-dichlorobiphenyl + O2
cis-5,6-dihydro-5,6-dihydroxy-2,2'-dichlorobiphenyl
show the reaction diagram
Burkholderia xenovorans
-
-
-
-
?
2,2'-difluorobiphenyl + O2
?
show the reaction diagram
2,2'-dihydroxybiphenyl + O2
6-(2-hydroxyphenyl)-6-oxohexa-2,4-dienoate
show the reaction diagram
2,2'-dinitrobiphenyl + O2
?
show the reaction diagram
2,3-dihydroxy-3'-chlorobiphenyl + O2
2-hydroxy-6-oxo-6-(3'-chlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
show the reaction diagram
2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O
show the reaction diagram
3',4',5'-trichloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(3',4',5'-trichlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
3',4'-dichloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(3',4'-dichlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
3',5'-dichloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(3',5'-dichlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
3'-chloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(3'-chlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
3,3'-dichlorobiphenyl + O2
?
show the reaction diagram
3,5-dichlorocatechol + O2
3,5-dichloro-2-hydroxy-6-oxohexa-2,4-dienoate
show the reaction diagram
3-chlorocatechol + O2
3-chloro-2-hydroxymuconic semialdehyde + H2O
show the reaction diagram
3-chlorocatechol + O2
?
show the reaction diagram
3-ethylcatechol + O2
2-hydroxy-7-methyl-6-oxoocta-2,4-dienoate
show the reaction diagram
3-formylcatechol + O2
?
show the reaction diagram
-
-
-
-
?
3-isoporopylcatechol + O2
2-hydroxy-7-methyl-6-oxo-octa-2,4-dienoate + ?
show the reaction diagram
-
relative activity 179%
-
-
?
3-isopropylcatechol + O2
2-hydroxy-7-methyl-6-oxo-octa-2,4-dienoate + ?
show the reaction diagram
-
-
-
-
?
3-methoxycatechol + O2
2-hydroxy-3-methoxy-6-oxohexa-2,4-dienoate
show the reaction diagram
-
relative activity 13%
-
-
?
3-methylcatechol + O2
2-hydroxy-6-oxohepta-2,4-dienoate
show the reaction diagram
3-methylcatechol + O2
?
show the reaction diagram
4'-chloro-2,3-dihydroxybiphenyl + O2
2-hydroxy-6-oxo-6-(4'-chlorophenyl)-hexa-2,4-dienoate + H2O
show the reaction diagram
4,4'-dichlorobiphenyl + O2
?
show the reaction diagram
4-chloro-2,3-dihydroxybiphenyl + O2
3-chloro-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
show the reaction diagram
4-chlorobiphenyl + O2
?
show the reaction diagram
-
-
-
-
?
4-chlorocatechol + O2
4-chloro-2-hydroxy-6-oxohexa-2,4-dienoate
show the reaction diagram
4-chlorocatechol + O2
?
show the reaction diagram
4-methylcatechol + O2
2-hydroxy-4-methyl-6-oxohexa-2,4-dienoate
show the reaction diagram
4-methylcatechol + O2
?
show the reaction diagram
biphenyl + O2
?
show the reaction diagram
biphenyl-2,3-diol + O2
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
show the reaction diagram
biphenyl-2,3-diol + O2
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O
show the reaction diagram
catechol + O2
2-hydroxymuconate semialdehyde
show the reaction diagram
catechol + O2
2-hydroxymuconic semialdehyde
show the reaction diagram
catechol + O2
?
show the reaction diagram
cis-5,6-dihydro-5,6-dihydroxy-2,2'-dichlorobiphenyl + O2
?
show the reaction diagram
Burkholderia xenovorans
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
biphenyl-2,3-diol + O2
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
show the reaction diagram
biphenyl-2,3-diol + O2
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
activates
Cu2+
activates
Fe
0.8 mol iron per mol subunit of BphC1; 1.0 mol iron per mol subunit of BphC1
Fe3+
1 mM, activates
Iron
-
ferrous enzyme
K+
activates
Manganese
enzyme contains 4.0-4.8 manganese atoms per enzyme molecule, depending on the batch
Ni2+
activates
Zn2+
activates
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
2,3-Dihydroxybiphenyl
2-Hydroxypyridine N-oxide
-
0.2 mM
3,4-dihydroxybiphenyl
-
strain CB406, inactivation in presence of O2
3-chlorocatechol
3-ethylcatechol
-
reversible substrate inhibition
3-methylcatechol
-
-
4-Chlorocatechol
-
-
4-Methylcatechol
-
-
8-hydroxyquinoline
5 mM 30 min
acetone
-
competitive inhibition
alpha,alpha'-dipyridyl
-
inhibits catalysis, but protects the Fe2+ from oxidative inactivation
Ba2+
1 mM, moderate inhibition
diethyldithiocarbamic acid
5 mM 30 min
Hg2+
1 mM, complete inhibition
iodoacetic acid
5 mM 30 min
isopropylalcohol
-
-
L-ascorbic acid
completely inhibits at concentrations over 25 mM
N-ethylmaleimide
5 mM 30 min
Ni2+
1 mM, strong inhibition
o-phenanthroline
-
-
tert-butanol
-
-
Zn2+
1 mM, complete inhibition with substrate biphenyl-2,3-diol, not with catechols
additional information
-
do not cleave 3,4-dihydroxybiphenyl, but is not inactivated
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.014
2'-aminobiphenyl-2,3-diol
-
pH 7.5, 25C
0.001 - 0.019
2'-chloro-2,3-dihydroxybiphenyl
0.0026
2,2'-dichlorobiphenyl
-
-
0.000095 - 0.74
2,3-Dihydroxybiphenyl
0.00045 - 0.01
3'-chloro-2,3-dihydroxybiphenyl
0.0033
3,3'-dichlorobiphenyl
-
-
0.007 - 0.03
3,5-dichlorocatechol
0.025 - 2.1
3-chlorocatechol
0.0108
3-formylcatechol
-
in 50 mM Hepes (pH 7.5) at 25C
0.001 - 14.6
3-methylcatechol
0.0015 - 0.012
4'-chloro-2,3-dihydroxybiphenyl
0.025 - 0.0496
4-Chlorocatechol
0.0273 - 93
4-Methylcatechol
0.0062
Biphenyl
-
-
0.00046 - 0.087
biphenyl-2,3-diol
0.0062 - 2.4
catechol
0.028 - 1.28
O2
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25 - 7.5
2'-chloro-2,3-dihydroxybiphenyl
4.8 - 84.1
2,3-Dihydroxybiphenyl
4 - 12
3'-chloro-2,3-dihydroxybiphenyl
9 - 15
3-chlorocatechol
0.8
3-formylcatechol
Pseudomonas sp.
-
in 50 mM Hepes (pH 7.5) at 25C
3 - 44
3-methylcatechol
4.5 - 18.8
4'-chloro-2,3-dihydroxybiphenyl
1
4-Chlorocatechol
Dyella ginsengisoli
A9QT35
pH 8.0, 20C
0.064 - 43.2
4-Methylcatechol
8.78 - 165
biphenyl-2,3-diol
0.016 - 52.56
catechol
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
250
2'-aminobiphenyl-2,3-diol
Pseudomonas resinovorans
-
pH 7.5, 25C
11777
4450
2,3-Dihydroxybiphenyl
Dyella ginsengisoli
A9QT35
pH 8.0, 20C
1584
89.8 - 10300
3-methylcatechol
20
4-Chlorocatechol
Dyella ginsengisoli
A9QT35
pH 8.0, 20C
1055
2 - 1582
4-Methylcatechol
224.6 - 40530
biphenyl-2,3-diol
24 - 8477
catechol
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3
2,3-Dihydroxybiphenyl
-
reversible substrate inhibition
0.22
3-chlorocatechol
-
-
11
3-ethylcatechol
-
-
13
acetone
-
-
35
ethanol
-
-
10.5
isopropylalcohol
-
-
5.2 - 9.9
tert-butanol
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.17
-
using 4-methylcatechol as substrate
0.33
-
using 1,2-dihydroxynaphthalene as substrate; using catechol as substrate
0.52
-
cell extract
1.88
-
using 1,2-dihydroxydibenzofuran as substrate
2.19
-
using 3-isopropylcatechol as substrate
3.1
-
BphC1
3.75
-
using 3-methylcatechol as substrate
4.79
-
using 2,3-dihydroxybiphenyl as substrate
6.88
-
after 13.2fold purification
57.3
-
strain OU83
118.3
with 2,3-dihydroxybiphenyl as substrate
additional information
-
no substrate specificity for 3,4-dihydroxybiphenyl, 2,3-dihydroxydibenzofuran, 3-chlorocatechol, 4-chlorocatechol, and pyrogallol
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 10
activity range, profile overview; activity range, profile overview; activity range, profile overview
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20
-
assay at
20 - 25
-
for meta-cleavage of 1,2-dihydroxydibenzofuran
50
recombinant enzyme
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 60
activity range, profile overview; activity range, profile overview; activity range, profile overview
20 - 80
activity range
20 - 70
20C: about 75% of maximal activity, 70C: about 85% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5
-
isoelectric focusing
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia xenovorans (strain LB400)
Burkholderia xenovorans (strain LB400)
Burkholderia xenovorans (strain LB400)
Burkholderia xenovorans (strain LB400)
Burkholderia xenovorans (strain LB400)
Burkholderia xenovorans (strain LB400)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
Pseudomonas sp. (strain KKS102)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
78000
-
heterotetramer, gel-filtration chromatography
125000
gel filtration
190000
gel filtration
220000
gel filtration
256000
-
gel filtration
265000
-
electron microscopy
270000
gel filtration
300000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterotetramer
hexamer
homotetramer
octamer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, using 30% (v/v) PEG 400, 200 mM magnesium chloride, 100 mM Tris-HCl pH 8.5 or 10% (v/v) 2-propanol, 100 mM MES-NaOH pH 6.5 and 200 mM zinc acetate
-
crystals grown from ammoinum sulfate and polyethylene glycol 6000, space groups of P42212 and I222
-
crystals diffract to 1.9 A reslution
-
space group R3, a = b = 136.35 A, c = 106.07 A
-
strain KKS102
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
-
-
659689
8.5
-
stable at
439412
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
no loss of activity after 24 h
37 - 65
loses 47% of the activity at 37C and all activity at 65C