Information on EC 1.3.1.56 - cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.3.1.56
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RECOMMENDED NAME
GeneOntology No.
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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redox reaction
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-
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
biphenyl degradation
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Dioxin degradation
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diphenyl ethers degradation
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Metabolic pathways
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Microbial metabolism in diverse environments
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SYSTEMATIC NAME
IUBMB Comments
cis-3-phenylcyclohexa-3,5-diene-1,2-diol:NAD+ oxidoreductase
Catalyses the second step in the biphenyl degradation pathway in bacteria.
CAS REGISTRY NUMBER
COMMENTARY hide
103289-54-9
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain LB400
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Manually annotated by BRENDA team
strain LB400
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Manually annotated by BRENDA team
i.e. Comamonas testosteroni strain B-356, gene bphB
UniProt
Manually annotated by BRENDA team
strain LB400
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme is involved in the aerobic biodegradation of polychlorinated biphenyls
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2,2',5,5'-tetrachlorobiphenyl + NAD+
2,2',5,5'-tetrachloro-3,4-dihydroxybiphenyl + NADH
show the reaction diagram
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
show the reaction diagram
7,2',3'-trihydroxy-8-methyl-2',3'-dihydro-isoflavone + NAD+
7,2',3'-trihydroxy-8-methylisoflavone + NADH
show the reaction diagram
7,3',4'-trihydroxy-3',4'-dihydro-isoflavone + NAD+
7,3',4'-trihydroxyisoflavone + NADH
show the reaction diagram
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recombinant enzyme
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-
?
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
show the reaction diagram
7-hydroxyisoflavone + 2 NAD+ + 2 H2O
7,3',4'-trihydroxyisoflavone + 2 NADH + 2 H+
show the reaction diagram
cis-1,2-dihydro-1,2-dihydroxynaphthalene + NAD+
? + NADH
show the reaction diagram
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-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
show the reaction diagram
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD(P)+
2,3-dihydroxybiphenyl + NAD(P)H
show the reaction diagram
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
show the reaction diagram
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
show the reaction diagram
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH + H+
show the reaction diagram
modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity
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?
cis-indole-2,3-dihydrodiol + NAD+
2,3-dihydroxyindole + NADH
show the reaction diagram
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isatin can be formed by spontaneously isomerization of 2,3-dihydroxyindole, which is formed from cis-indole-2,3-dihydrodiol catalyzed by BphB
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?
additional information
?
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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
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
show the reaction diagram
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
show the reaction diagram
7-hydroxyisoflavone + 2 NAD+ + 2 H2O
7,3',4'-trihydroxyisoflavone + 2 NADH + 2 H+
show the reaction diagram
cis-1,2-dihydro-1,2-dihydroxynaphthalene + NAD+
? + NADH
show the reaction diagram
Q46381
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
show the reaction diagram
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD(P)+
2,3-dihydroxybiphenyl + NAD(P)H
show the reaction diagram
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second step of the metabolic pathway for the bacterial degradation of biphenyl
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
show the reaction diagram
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
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NADP+ is a poor cofactor, probably due to Asp at position 36
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.073
2,3-dihydro-2,3,-dihydroxybiphenyl
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activity measured with 1 micromol NAD+ in the reaction mixture at pH 9.5 and 37°C
1.5
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl
with 2.5 mM NAD+
0.28
cis-1,2-dihydro-1,2-dihydroxynaphthalene
with 2.5 mM NAD+
0.0031 - 0.0039
cis-2,3-dihydro-2,3-dihydroxybiphenyl
0.00024
NAD(P)+
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at pH 9 and 25°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.123
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl
Comamonas testosteroni
Q46381
with 2.5 mM NAD+
0.9
cis-1,2-dihydro-1,2-dihydroxynaphthalene
Comamonas testosteroni
Q46381
with 2.5 mM NAD+
0.38
cis-2,3-dihydro-2,3-dihydroxybiphenyl
Comamonas testosteroni
Q46381
with 2.5 mM NAD+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17.4
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after purification at 25°C and pH 9
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at, medium for in vivo experiments
9.5
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recombinant His-tagged enzyme
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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assay at, cell culture temperature for in vivo experiments
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
123000
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native protein, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant detagged BphB, sitting drop vapour diffusion method, 0.001 ml of 10 mg/ml protein in 20 mM HEPES, pH 8.0, 10% glycerol, and 300 mM NaCl, are mixed with 0.001 ml of reservoir solution containing 0.2 M sodium malonate, pH 6.0, and 20% PEG 3350, 20% glycerol is used as cryoprotectant, X-ray diffractiuon structure determination and analysis at 2.8 A resolution
the crystal structures of the apoenzyme, the binary complex with NAD+, and the ternary complexes with NAD-2,3-dihydroxybiphenyl and NAD+-4,4'-dihydroxybiphenyl are determined at 2.2-, 2.5-, 2.4-, and 2.1 A resolutions, respectively. A series of conformational changes in the substrate binding loop that occur during ligand binding are identified
the crystal structure of the NAD+-enzyme complex is determined by molecular replacement and refined to an R-value of 17.9% at 2.0 A
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C stable in 50% glycerol for months
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-70°C for months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, DEAE-Sepharose chromatography, yield about 50 mg of enzyme/l of cell culture
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recombinant His-tagged BphB from Escherichia coli strain BL21 (DE3) to homogeneity by niockel affinity chromatography, the His-tag is cleaved off followed by ultrafiltration and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
functional coexpression of enzymes BphB and BphA in Escherichia coli, gene construct bphA1A2A3A4B in the plasmid vector
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gene bphB, overexpression of N-terminally His-tagged BphB in Escherichia coli strain BL21 (DE3)
the genes encoding biphenyl dioxygenase (BphA) and biphenyl-2,3-dihydrodiol 2,3-dehydrogenase (BphB) are cloned from Dyella ginsengisoli LA-4 and heterologously expressed in Escherichia coli. The feasibility of indole transformation to indigo by strain BphA LA-4 is predicted by molecular docking studies
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