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Information on EC 1.3.1.56 - cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase and Organism(s) Comamonas testosteroni and UniProt Accession Q46381

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IUBMB Comments
Catalyses the second step in the biphenyl degradation pathway in bacteria.
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This record set is specific for:
Comamonas testosteroni
UNIPROT: Q46381
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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-2,3-dihydrodiol-2,3-dehydrogenase, b2,3d, cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase, biphenyl dehydrogenase, cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase, 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase, 2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase, biphenyl-2,3-dihydrodiol 2,3-dehydrogenase, nad-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biphenyl dehydrogenase
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biphenyl dihydrodiol dehydrogenase
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cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
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2,3-dihydro-2,3-dehydroxybiphenyl-2,3-dehydrogenase
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2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
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2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase
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B2,3D
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Biphenyl-2,3-dihydro-2,3-diol dehydrogenase
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biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
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Biphenyl-cis-diol dehydrogenase
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-
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cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
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additional information
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
catalytic triad is formed by the conserved residues SEr142, Tyr153, and Lys159
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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-
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oxidation
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-
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reduction
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-
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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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SUBSTRATE
PRODUCT                       
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
cis-1,2-dihydro-1,2-dihydroxynaphthalene + NAD+
? + NADH
show the reaction diagram
-
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
show the reaction diagram
2,2',5,5'-tetrachlorobiphenyl + NAD+
2,2',5,5'-tetrachloro-3,4-dihydroxybiphenyl + NADH
show the reaction diagram
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-
-
-
?
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
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-
-
-
?
additional information
?
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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
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
-
-
?
cis-1,2-dihydro-1,2-dihydroxynaphthalene + NAD+
? + NADH
show the reaction diagram
-
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
show the reaction diagram
biphenyl degradation pathway
-
?
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
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biphenyl degradation pathway
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?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
show the reaction diagram
-
-
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?
additional information
?
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enzyme catalyzes the second step in the biphenyl catabolic degradation pathway, substrate spectrum of the organism in vivo, overview
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
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
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+
0.0039
cis-2,3-dihydro-2,3-dihydroxybiphenyl
with 2.5 mM NAD+
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
0.0031
cis-2,3-dihydro-2,3-dihydroxybiphenyl
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at pH 9 and 25°C
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
with 2.5 mM NAD+
0.9
cis-1,2-dihydro-1,2-dihydroxynaphthalene
with 2.5 mM NAD+
0.38
cis-2,3-dihydro-2,3-dihydroxybiphenyl
with 2.5 mM NAD+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17.4
-
after purification at 25°C and pH 9
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9.5
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recombinant His-tagged enzyme
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?
BPHB_COMTE
281
0
29350
Swiss-Prot
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29400
x * 29400, about
123000
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native protein, gel filtration
29400
-
4 * 29400, electrospray mass spectrometry
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 29400, about
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
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
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
ammonium sulfate precipitation, DEAE-Sepharose chromatography, yield about 50 mg of enzyme/l of cell culture
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene bphB, overexpression of N-terminally His-tagged BphB in Escherichia coli strain BL21 (DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Vedadi, M.; Barriault, D.; Sylvestre, M; Powlowski, J.
Active site residues of cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from Comamonas testosteroni strain B-356
Biochemistry
39
5028-5034
2000
Comamonas testosteroni
Manually annotated by BRENDA team
Sylvestre, M.; Hurtubise, Y.; Barriault, D.; Bergeron, J.; Ahmad, D.
Characterization of active recombinant 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from Comamonas testosteroni B-356 and sequence of the encoding gene (bphB)
Appl. Environ. Microbiol.
62
2710-2715
1996
Comamonas testosteroni
Manually annotated by BRENDA team
Barriault, D.; Vedadi, M.; Powlowski, J.; Sylvestre, M.
cis-2,3-Dihydro-2,3-dihydroxybiphenyl dehydrogenase and cis-1,2-dihydro-1,2-dihydroxynaphathalene dehydrogenase catalyze dehydrogenation of the same range of substrates
Biochem. Biophys. Res. Commun.
260
181-187
1999
Burkholderia cepacia, Burkholderia cepacia LB400, Comamonas testosteroni (Q46381), Comamonas testosteroni
Manually annotated by BRENDA team
Sylvestre, M.
Genetically modified organisms to remediate polychlorinated biphenyls. Where do we stand?
Int. Biodeter. Biodegrad.
54
153-162
2004
Burkholderia sp., Burkholderia sp. LB400, Comamonas testosteroni
-
Manually annotated by BRENDA team
Patil, D.N.; Tomar, S.; Sylvestre, M.; Kumar, P.
Expression, purification, crystallization and preliminary crystallographic studies of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from Pandoraea pnomenusa B-356
Acta Crystallogr. Sect. F
66
1517-1520
2010
Comamonas testosteroni (Q46381), Comamonas testosteroni B-356 (Q46381)
Manually annotated by BRENDA team
Dhindwal, S.; Patil, D.N.; Mohammadi, M.; Sylvestre, M.; Tomar, S.; Kumar, P.
Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme
J. Biol. Chem.
286
37011-37022
2011
Comamonas testosteroni (Q46381)
Manually annotated by BRENDA team