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Information on EC 1.3.1.56 - cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
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1.3.1.56 cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenaseIUBMB Comments
Catalyses the second step in the biphenyl degradation pathway in bacteria.
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Word Map
- 1.3.1.56
- biphenyls
- dioxygenase
-
polychlorinated
- testosteroni
-
comamonas
- pnomenusa
-
burkholderia
-
pandoraea
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chlorinated
-
chlorobiphenyls
-
congener
-
dehydrogenation
- toluene
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bpha1a2a3a4
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cis-dihydrodiols
- cepacia
-
meta-cleavage
- dehydrogenases
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ortho-substituted
- putida
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2,2\',5,5\'-tetrachlorobiphenyl
The enzyme appears in viruses and cellular organisms
Reaction Schemes
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, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2,3-dihydro-2,3-dehydroxybiphenyl-2,3-dehydrogenase
2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
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-
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2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase
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B2,3D
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biphenyl dihydrodiol dehydrogenase
Biphenyl-2,3-dihydro-2,3-diol dehydrogenase
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biphenyl-2,3-dihydrodiol 2,3-dehydrogenase
biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
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Biphenyl-cis-diol dehydrogenase
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BphB
BphBB356
cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
additional information
cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
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-
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additional information
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enzyme belongs to the short-chain alcohol dehydrogenase/reductase family
additional information
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enzyme belongs to the short-chain alcohol dehydrogenase/reductase family
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additional information
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enzyme belongs to the short-chain alcohol dehydrogenase/reductase family
additional information
the enzyme belongs to the short-chain alcohol dehydrogenase/reductase, SDR, family
additional information
the enzyme belongs to the short-chain alcohol dehydrogenase/reductase, SDR, family
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH + H+
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-
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cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH + H+
catalytic triad is formed by the conserved residues SEr142, Tyr153, and Lys159
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cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH + H+
a two-step reaction mechanism is proposed
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
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redox reaction
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reduction
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PATHWAY SOURCE
PATHWAYS
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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.
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CAS REGISTRY NUMBER
COMMENTARY
103289-54-9
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
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
7,2',3'-trihydroxy-8-methyl-2',3'-dihydro-isoflavone + NAD+
7,2',3'-trihydroxy-8-methylisoflavone + NADH
7,3',4'-trihydroxy-3',4'-dihydro-isoflavone + NAD+
7,3',4'-trihydroxyisoflavone + NADH
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recombinant enzyme
-
-
?
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
cis-1,2-dihydro-1,2-dihydroxynaphthalene + NAD+
? + NADH
-
-
?
cis-indole-2,3-dihydrodiol + NAD+
2,3-dihydroxyindole + NADH
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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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-
?
2,2',5,5'-tetrachlorobiphenyl + NAD+
2,2',5,5'-tetrachloro-3,4-dihydroxybiphenyl + NADH
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-
-
-
?
2,2',5,5'-tetrachlorobiphenyl + NAD+
2,2',5,5'-tetrachloro-3,4-dihydroxybiphenyl + NADH
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-
-
-
?
2,2',5,5'-tetrachlorobiphenyl + NAD+
2,2',5,5'-tetrachloro-3,4-dihydroxybiphenyl + NADH
-
-
-
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
-
?
7,2',3'-trihydroxy-8-methyl-2',3'-dihydro-isoflavone + NAD+
7,2',3'-trihydroxy-8-methylisoflavone + NADH
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recombinant enzyme
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-
?
7,2',3'-trihydroxy-8-methyl-2',3'-dihydro-isoflavone + NAD+
7,2',3'-trihydroxy-8-methylisoflavone + NADH
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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+
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2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
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-
?
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
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2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
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-
?
7-hydroxyisoflavone + 2 NAD+ + 2 H2O
7,3',4'-trihydroxyisoflavone + 2 NADH + 2 H+
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2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
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-
?
7-hydroxyisoflavone + 2 NAD+ + 2 H2O
7,3',4'-trihydroxyisoflavone + 2 NADH + 2 H+
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2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
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-
?
cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl + NAD+
?
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
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-
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
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polychlorobiphenyl catabolic pathway
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
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-
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
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polychlorobiphenyl catabolic pathway
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD(P)+
2,3-dihydroxybiphenyl + NAD(P)H
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-
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD(P)+
2,3-dihydroxybiphenyl + NAD(P)H
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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
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
-
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
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biphenyl degradation pathway
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?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
biphenyl degradation pathway
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?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
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-
-
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?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
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-
-
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
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-
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?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH + H+
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?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH + H+
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-
-
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH + H+
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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?
additional information
?
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biotransformation of natural and synthetic isoflavonoids by the recombinant enzyme, overview
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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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-
?
additional information
?
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enzyme shows a broad substrate specificity
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?
additional information
?
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enzyme shows a broad substrate specificity
-
-
?
additional information
?
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biotransformation of natural and synthetic isoflavonoids by the recombinant enzyme, overview
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-
?
additional information
?
-
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enzyme shows a broad substrate specificity
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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
-
-
?
additional information
?
-
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enzyme shows a broad substrate specificity
-
-
?
additional information
?
-
-
enzyme catalyzes the second step in the biphenyl catabolic degradation pathway, substrate spectrum of the organism in vivo, overview
-
-
?
additional information
?
-
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enzyme shows a broad substrate specificity
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
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
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
cis-1,2-dihydro-1,2-dihydroxynaphthalene + NAD+
? + NADH
-
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD(P)+
2,3-dihydroxybiphenyl + NAD(P)H
-
second step of the metabolic pathway for the bacterial degradation of biphenyl
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
-
?
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NAD+
3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl + NADH
-
-
?
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
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2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
-
-
?
7-hydroxy-8-methylisoflavone + 2 NAD+ + 2 H2O
7,2',3'-trihydroxy-8-methylisoflavone + 2 NADH + 2 H+
-
2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
-
-
?
7-hydroxyisoflavone + 2 NAD+ + 2 H2O
7,3',4'-trihydroxyisoflavone + 2 NADH + 2 H+
-
2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
-
-
?
7-hydroxyisoflavone + 2 NAD+ + 2 H2O
7,3',4'-trihydroxyisoflavone + 2 NADH + 2 H+
-
2-step biotransformation in cooperation with biphenyl-2,3-dioxygenase, BphA, catalyzing the first step and BphB the second step, recombinant enzymes in Escherichia coli cells
-
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
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polychlorobiphenyl catabolic pathway
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + ?
2,3-dihydroxybiphenyl + ?
-
polychlorobiphenyl catabolic pathway
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
-
biphenyl degradation pathway
-
?
cis-2,3-dihydro-2,3-dihydroxybiphenyl + NAD+
2,3-dihydroxybiphenyl + NADH
biphenyl degradation pathway
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
-
-
-
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
-
-
-
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH
-
-
-
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH + H+
-
-
-
-
?
cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
biphenyl-2,3-diol + NADH + H+
-
-
-
-
?
additional information
?
-
-
biotransformation of natural and synthetic isoflavonoids by the recombinant enzyme, overview
-
-
?
additional information
?
-
-
enzyme catalyzes the second step in the biphenyl catabolic degradation pathway, substrate spectrum of the organism in vivo, overview
-
-
?
additional information
?
-
-
biotransformation of natural and synthetic isoflavonoids by the recombinant enzyme, overview
-
-
?
additional information
?
-
-
enzyme catalyzes the second step in the biphenyl catabolic degradation pathway, substrate spectrum of the organism in vivo, overview
-
-
?
additional information
?
-
-
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
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
LITERATURE
IMAGE
0.073
2,3-dihydro-2,3,-dihydroxybiphenyl
-
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+
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.123
3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl
with 2.5 mM NAD+
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
-
PbBphB is a member of the short-chain dehydrogenase/reductase (SRD) family
evolution
-
PbBphB is a member of the short-chain dehydrogenase/reductase (SRD) family
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metabolism
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NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB) catalyzes the second step of the PCB catabolic pathway in bacteria
metabolism
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NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB) catalyzes the second step of the PCB catabolic pathway in bacteria
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physiological function
the enzyme is involved in the aerobic biodegradation of polychlorinated biphenyls
physiological function
-
the enzyme is the key enzyme in the biphenyl/polychlorinated biphenyl catabolic pathway
physiological function
-
the enzyme is the key enzyme in the biphenyl/polychlorinated biphenyl catabolic pathway
-
additional information
-
the pocket between strand beta6 and helix alpha8 is the substrate-binding region and corresponds to a disordered region (Leu199-Ser206) in the structures of the apo and binary forms, dynamic behavior of the substrate binding loop. In the holo form, BPY stabilizes the conformation of the binding loop by interacting through the aromatic rings of reaction product 2,3-dihydroxybiphenyl with Val207 and Pro208 residues. Ile204 makes a hydrophobic interaction with the NAD+ cofactor only in the holo simulation. The lack of the latter interaction in the apo and in the binary forms explains the extended mobility of this region in the other two binding states of the protein
additional information
-
the pocket between strand beta6 and helix alpha8 is the substrate-binding region and corresponds to a disordered region (Leu199-Ser206) in the structures of the apo and binary forms, dynamic behavior of the substrate binding loop. In the holo form, BPY stabilizes the conformation of the binding loop by interacting through the aromatic rings of reaction product 2,3-dihydroxybiphenyl with Val207 and Pro208 residues. Ile204 makes a hydrophobic interaction with the NAD+ cofactor only in the holo simulation. The lack of the latter interaction in the apo and in the binary forms explains the extended mobility of this region in the other two binding states of the protein
-
Show AA Sequence and Transmembrane Helices (122 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
29400
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
tetramer
additional information
additional information
-
three-dimensional enzyme structure analysis, crystal structure analysis of PpBphB, PDB ID 3ZV5, molecular dynamics simulations, overview
additional information
-
three-dimensional enzyme structure analysis, crystal structure analysis of PpBphB, PDB ID 3ZV5, molecular dynamics simulations, overview
-
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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
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE