Information on EC 1.4.5.1 - D-amino acid dehydrogenase (quinone)

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.4.5.1
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RECOMMENDED NAME
GeneOntology No.
D-amino acid dehydrogenase (quinone)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a D-amino acid + H2O + a quinone = a 2-oxo carboxylate + NH3 + a quinol
show the reaction diagram
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Phenylalanine metabolism
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SYSTEMATIC NAME
IUBMB Comments
D-amino acid:quinone oxidoreductase (deaminating)
An iron-sulfur flavoprotein (FAD). The enzyme from the bacterium Helicobacter pylori is highly specific for D-proline, while the enzyme from the bacterium Escherichia coli B is most active with D-alanine, D-phenylalanine and D-methionine. This enzyme may be the same as EC 1.4.99.6.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
strain UMM5 (putA1::Tn5 proC24)
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Manually annotated by BRENDA team
NCTC 11637
SwissProt
Manually annotated by BRENDA team
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-dehydro-DL-proline + oxidized 2,6-dichloroindophenol
?
show the reaction diagram
beta-chloro-D-alanine + oxidized acceptor + H2O
? + NH3 + reduced acceptor
show the reaction diagram
-
assayed in toluenized cells, reaction rate is 20% of the activity with D-alanine
-
-
?
D-2-amino-n-butyrate + oxidized 2,6-dichlorophenolindophenol + H2O
2-oxobutyrate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
D-Ala + oxidized coenzyme Q1 + H2O
pyruvate + NH3 + reduced coenzyme Q1
show the reaction diagram
specific activity is 37% of that with D-proline
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-
?
D-alanine + oxidized 2,6-dichloroindophenol + H2O
pyruvate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
D-alanine + oxidized acceptor
pyruvate + NH3 + reduced acceptor
show the reaction diagram
-
the enzyme couples D-alanine oxidation to solute active transport in Escherichia coli B cytoplasmic membrane vesicles
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-
?
D-alanine + oxidized acceptor + H2O
pyruvate + NH3 + reduced acceptor
show the reaction diagram
D-alanine + oxidized coenzyme Q1
pyruvate + NH3 + reduced coenzyme Q1
show the reaction diagram
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no activity with menaquinone or adriamycin
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-
?
D-arginine + oxidized 2,6-dichlorophenolindophenol + H2O
2-oxo-5-guanidinopentanoate + NH3 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
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41% of the activity with D-alanine
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-
?
D-arginine + oxidized acceptor + H2O
2-oxo-5-guanidinopentanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 2.9% of the activity with D-alanine
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-
?
D-asparagine + oxidized 2,6-dichlorophenolindophenol + H2O
2-oxosuccinamic acid + NH3 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
D-asparagine + oxidized acceptor + H2O
2-oxosuccinamic acid + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 21% of the activity with D-alanine
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-
?
D-cycloserine + oxidized 2,6-dichloroindophenol + H2O
?
show the reaction diagram
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as a active as D-alanine
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?
D-cysteine + oxidized acceptor
? + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 4.1% of the activity with D-alanine
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?
D-ethionine + oxidized acceptor + H2O
? + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 41% of the activity with D-alanine
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?
D-glutamine + oxidized 2,6-dichloroindophenol + H2O
4-carbamoyl-2-oxobutanoate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
D-histidine + oxidized 2,6-dichloroindophenol + H2O
3-(1H-imidazol-4-yl)-2-oxopropanoate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
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8.5% of the activity compared to D-alanine
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?
D-histidine + oxidized acceptor + H2O
3-(1H-imidazol-4-yl)-2-oxopropanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 12% of the activity with D-alanine
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?
D-leucine + oxidized acceptor + H2O
4-methyl-2-oxopentanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 20% of the activity with D-alanine
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-
?
D-methionine + oxidized 2,6-dichloroindophenol + H2O
4-methylsulfanyl-2-oxobutanoate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
D-methionine + oxidized 2,6-dichlorophenolindophenol + H2O
4-methylsulfanyl-2-oxobutanoate + NH3 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
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70% of the activity with D-alanine
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-
?
D-methionine + oxidized acceptor + H2O
4-methylsulfanyl-2-oxobutanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 39% of the activity with D-alanine
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-
?
D-Phe + oxidized coenzyme Q1 + H2O
phenylpyruvate + NH3 + reduced coenzyme Q1
show the reaction diagram
specific activity is 20% of that with D-proline
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?
D-phenylalanine + oxidized 2,6-dichloroindophenol + H2O
phenylpyruvate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
D-phenylalanine + oxidized acceptor + H2O
phenylpyruvate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 72% of the activity with D-alanine
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?
D-proline + oxidized 2,6-dichloroindophenol
DELTA1-pyrroline-2-carboxylate + reduced 2,6-dichloroindophenol
show the reaction diagram
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28% of the activity compared to D-alanine
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?
D-proline + oxidized 2,6-dichlorophenolindophenol
DELTA1-pyrroline-2-carboxylate + NH3 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
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19% of the activity with D-alanine
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?
D-proline + oxidized acceptor
DELTA1-pyrroline-2-carboxylate + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 2.6% of the activity with D-alanine
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?
D-proline + oxidized coenzyme Q1 + H2O
DELTA1-pyrroline-2-carboxylate + NH3 + reduced coenzyme Q1
show the reaction diagram
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-
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?
D-Ser + oxidized coenzyme Q1 + H2O
3-hydroxy-2-oxopropanoate + NH3 + reduced coenzyme Q1
show the reaction diagram
specific activity is 7% of that with D-proline
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?
D-serine + oxidized 2,6-dichloroindophenol + H2O
3-hydroxy-2-oxopropanoate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
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29% of the activity compared to D-alanine
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?
D-serine + oxidized 2,6-dichlorophenolindophenol + H2O
3-hydroxy-2-oxopropanoate + NH3 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
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20% of the activity compared to D-alanine
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?
D-serine + oxidized acceptor + H2O
3-hydroxy-2-oxopropanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 13% of the activity with D-alanine
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?
D-threonine + H2O + oxidized acceptor
3-hydroxy-2-oxobutanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 5.9% of the activity with D-alanine
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?
D-valine + oxidized 2,6-dichloroindophenol + H2O
2-oxoisopentanoate + NH3 + reduced 2,6-dichloroindophenol
show the reaction diagram
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11% of the activity compared to D-alanine
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?
D-valine + oxidized 2,6-dichlorophenolindophenol + H2O
2-oxoisopentanoate + NH3 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
26% of the activity with D-alanine
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?
D-valine + oxidized acceptor + H2O
2-oxoisopentanoate + NH3 + reduced acceptor
show the reaction diagram
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assayed in toluenized cells, reaction rate is 2.6% of the activity with D-alanine
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?
additional information
?
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activity with D-Val, D-Met, D-Glu, D-Asp, L-Pro and L-Ala is below 5% of the activity with D-Pro
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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-dehydro-DL-proline + oxidized 2,6-dichloroindophenol
?
show the reaction diagram
D-alanine + oxidized acceptor
pyruvate + NH3 + reduced acceptor
show the reaction diagram
-
the enzyme couples D-alanine oxidation to solute active transport in Escherichia coli B cytoplasmic membrane vesicles
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-
?
D-alanine + oxidized acceptor + H2O
pyruvate + NH3 + reduced acceptor
show the reaction diagram
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the enzyme is inducible by L-alanine and repressible by glucose
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ubiquinone
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol fold
ubiquinone-0
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 16fold
ubiquinone-1
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 25fold
ubiquinone-2
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 26fold
ubiquinone-3
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 21fold
ubiquinone-4
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 3fold
ubiquinone-5
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 2fold
ubiquinone-6
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 2fold
ubiquinone-7
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 2fold
ubiquinone-8
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0.2 mM quinone stimulates reaction with D-alanine and oxidized 2,6-dichloroindophenol 2fold
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
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iron-sulfur flavoprotein
additional information
Mg2+ and Ca2+ have no effect on DadA activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Benzoate
0.1 mM, 98% inhibition
D-alanine
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oxidation of 3,4-dehydro-DL-proline by membrane fractions from strain UMM5 is competitively inhibited by D-alanine
iodoacetamide
0.1 mM, 66% inhibition
iodoacetic acid
0.1 mM, 62% inhibition
menaquinone
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p-hydroxybenzoic acid
0.1 mM, 79% inhibition
additional information
EDTA, Mg2+ and Ca2+ have no effect on DadA activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.01
2,6-dichlorophenolindophenol
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coenzyme Q mediated
12
D-2-amino-n-butyrate
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with 2,6-dichlorophenolindophenol
2 - 53
D-alanine
200
D-cycloserine
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14 - 71
D-glutamine
11
D-methionine
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with 2,6-dichlorophenolindophenol
6
D-phenylalanine
-
with 2,6-dichlorophenolindophenol
40 - 40.2
D-proline
19
D-serine
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with 2,6-dichlorophenolindophenol
0.63
oxidized 2,6-dichlorophenolindophenol
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with D-alanine
0.0082
oxidized coenzyme Q1
pH 8.0, 37C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15.7
D-2-amino butyrate
Escherichia coli B
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15.5
D-alanine
Escherichia coli B
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3.17
D-glutamine
Escherichia coli B
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16
D-methionine
Escherichia coli B
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14.7
D-phenylalanine
Escherichia coli B
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8.33
D-proline
Escherichia coli B
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5.33
D-serine
Escherichia coli B
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.9
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substrate: D-alanine, solubilized enzyme
8.9
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substrate: D-alanine, native enzyme
9
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oxidation of 3,4-dehydro-DL-proline by membrane fractions from strain UMM5 has a pH optimum of 9
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.5
pH 7.5: about 50% of maximal activity, pH 8.5: about 45% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 55
25C: about 50% of maximal activity, 55C: about 65% of maximal activity
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
49000
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SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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1 * 49000, SDS-PAGE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
42
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10 min, solubilized enzyme loses 95% of its activity, the native enzyme loses 49% of its activity
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
association with the membrane bilayer protects the enzyme against thermal denaturation
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 0.1 M potassium phosphate, pH 7.5, 0.02% Triton X-100, more than 1 mg protein/ml, stable for at least 3 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
from Helicobacter pylori and recombinant Escherichia coli cells
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli