Information on EC 2.6.1.21 - D-amino-acid transaminase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
2.6.1.21
-
RECOMMENDED NAME
GeneOntology No.
D-amino-acid transaminase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-alanine + 2-oxoglutarate = pyruvate + D-glutamate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amino group transfer
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
alanine metabolism
-
-
Arginine and proline metabolism
-
-
D-Alanine metabolism
-
-
D-Arginine and D-ornithine metabolism
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Lysine degradation
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Metabolic pathways
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Phenylalanine metabolism
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SYSTEMATIC NAME
IUBMB Comments
D-alanine:2-oxoglutarate aminotransferase
A pyridoxal-phosphate protein. The enzyme from thermophilic Bacillus species acts on many D-amino acids with D-alanine and D-2-aminobutyrate as the best amino donors. It can similarly use any of several 2-oxo acids as amino acceptor, with 2-oxoglutarate and 2-oxobutyrate among the best. The enzyme from some other sources has a broader specificity [6].
CAS REGISTRY NUMBER
COMMENTARY hide
37277-85-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
YM-1, thermophile
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-
Manually annotated by BRENDA team
Neosartorya fischeri
-
-
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Manually annotated by BRENDA team
var Alaska
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-
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
1-(4-nitrophenyl)ethanone + D-alanine
(1R)-1-(4-nitrophenyl)ethanamine + pyruvate
show the reaction diagram
1-cyclohexylethanone + D-alanine
(1R)-1-cyclohexylethanamine + pyruvate
show the reaction diagram
1-phenylethanone + D-alanine
(1R)-1-phenylethanamine + pyruvate
show the reaction diagram
4-(3-hydroxy-4-methoxyphenyl)butan-2-one + D-alanine
5-[(3R)-3-aminobutyl]-2-methoxyphenol + pyruvate
show the reaction diagram
4-(4-hydroxyphenyl)butan-2-one + D-alanine
4-[(3R)-3-aminobutyl]phenol + pyruvate
show the reaction diagram
4-(4-methoxyphenyl)butan-2-one + D-alanine
(2R)-2-amino-4-(4-methoxyphenyl)butane + pyruvate
show the reaction diagram
4-methylpentan-2-one + D-alanine
(2R)-2-amino-4-methylpentane + pyruvate
show the reaction diagram
4-phenylbutan-2-one + D-alanine
(2R)-2-amino-4-phenylbutane + pyruvate
show the reaction diagram
beta-chloro-D-alanine
pyruvate + ammonia + Cl-
show the reaction diagram
-
loss in enzyme activity during beta-elimination
-
?
D-2-aminobutanoate + pyruvate
2-oxobutanoate + D-alanine
show the reaction diagram
D-alanine + 2-oxobutanoate
pyruvate + 2-aminobutanoate
show the reaction diagram
-
-
-
r
D-alanine + 2-oxoglutarate
pyruvate + D-glutamate
show the reaction diagram
D-alanine + 2-oxoisovalerate
pyruvate + D-valine
show the reaction diagram
-
-
-
?
D-alanine + pyruvate
pyruvate + D-alanine
show the reaction diagram
-
-
-
?
D-aminobutanoate + 2-oxoglutarate
oxobutanoate + D-glutamate
show the reaction diagram
D-arginine + 2-oxoglutarate
? + D-glutamate
show the reaction diagram
-
6% of the activity with D-alanine
-
?
D-asparagine + 2-oxoglutarate
2-oxosuccinamate + D-glutamate
show the reaction diagram
D-asparagine + pyruvate
2-oxosuccinamate + D-alanine
show the reaction diagram
D-aspartate + 2-oxoglutarate
2-oxosuccinate + D-glutamate
show the reaction diagram
D-aspartate + pyruvate
2-oxosuccinate + D-alanine
show the reaction diagram
D-ethionine + 2-oxoglutarate
4-ethylsulfanyl-2-oxobutanoate + D-glutamate
show the reaction diagram
-
76% of the activity with D-alanine
-
?
D-glutamate + 2-oxobutanoate
2-oxoglutarate + 2-aminobutanoate
show the reaction diagram
D-glutamate + 2-oxoglutarate
2-oxoglutarate + D-glutamate
show the reaction diagram
D-glutamate + pyruvate
2-oxoglutarate + D-alanine
show the reaction diagram
D-glutamine + 2-oxoglutarate
4-carbamoyl-2-oxobutanoate + D-glutamate
show the reaction diagram
D-glutamine + pyruvate
4-carbamoyl-2-oxobutanoate + D-alanine
show the reaction diagram
-
-
-
?
D-histidine + 2-oxoglutarate
3-(1H-imidazol-4-yl)-2-oxopropanoate + L-glutamate
show the reaction diagram
-
6% of the activity with D-alanine
-
?
D-leucine + 2-oxoglutarate
4-methyl-2-oxopentanoate + D-glutamate
show the reaction diagram
-
8% of the activity with D-alanine
-
?
D-lysine + pyruvate
? + D-alanine
show the reaction diagram
D-methionine + 2-oxoglutarate
4-methylsulfanyl-2-oxobutanoate + D-glutamate
show the reaction diagram
D-methionine + pyruvate
4-methylsulfanyl-2-oxobutanoate + L-alanine
show the reaction diagram
D-norleucine + 2-oxoglutarate
2-oxopentanoate + D-glutamate
show the reaction diagram
D-norleucine + pyruvate
2-oxopentanoate + D-alanine
show the reaction diagram
-
-
-
?
D-norvaline + 2-oxoglutarate
2-oxopentanoate + D-glutamate
show the reaction diagram
D-norvaline + pyruvate
2-oxopentanoate + D-alanine
show the reaction diagram
D-ornithine + 2-oxoglutarate
? + D-glutamate
show the reaction diagram
D-ornithine + pyruvate
? + L-alanine
show the reaction diagram
D-phenylalanine + 2-oxoglutarate
phenylpyruvate + D-glutamate
show the reaction diagram
D-phenylalanine + pyruvate
phenylpyruvate + D-alanine
show the reaction diagram
D-serine + 2-oxoglutarate
3-hydroxy-2-oxopropanoate + D-glutamate
show the reaction diagram
D-serine + pyruvate
3-hydroxy-2-oxopropanoate + D-alanine
show the reaction diagram
-
-
-
?
D-theanine + 2-oxoglutarate
? + D-glutamate
show the reaction diagram
-
40% of the activity with D-alanine
-
?
D-tryptophan + 2-oxoglutarate
3-indole-2-oxopropanoate + D-glutamate
show the reaction diagram
D-tryptophan + pyruvate
3-indole-2-oxopropanoate + D-alanine
show the reaction diagram
D-valine + 2-oxoglutarate
2-oxoisovalerate + D-glutamate
show the reaction diagram
-
5% of activity with D-alanine
-
?
D-valine + pyruvate
2-oxoisovalerate + D-alanine
show the reaction diagram
-
-
-
?
heptan-2-one + D-alanine
(2R)-2-aminoheptane + pyruvate
show the reaction diagram
hexan-2-one + D-alanine
(2R)-2-aminohexane + pyruvate
show the reaction diagram
nonan-2-one + D-alanine
(2R)-2-aminononane + pyruvate
show the reaction diagram
pentan-2-one + D-alanine
(2R)-2-aminopentane + pyruvate
show the reaction diagram
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
D-alanine + 2-oxoglutarate
pyruvate + D-glutamate
show the reaction diagram
-
function of the enzyme is probably the provision of D-amino acids for cell-wall synthesis
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-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-Amino-3-butenoate
3-Methyl-2-benzothiazolone hydrazone hydrochloride
-
-
aminooxyacetic acid
-
0.0001 mM, 50% inhibition
Aminoxyacetate
-
0.01 mM, 90% inhibition
beta-Chloro-D-alanine
CaCl2
-
45 mM, 50% inhibition
cysteine
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inhibition of D- and L-transamination of D-alanine to 2-oxoglutarate
D-2-Aminobutanoate
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inhibition of D- and L-transamination of D-alanine to 2-oxoglutarate, weak
D-asparagine
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inhibition of D- and L-transamination of D-alanine to alpha-ketoglutarate, weak
D-Aspartate
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inhibition of D- and L-transamination of D-alanine to 2-oxoglutarate, weak
D-cycloserine
D-Cysteine
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0.1 mM, 60% inhibition
D-glutamate
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competitive to D-alanine, noncompetitive to 2-oxoglutarate
D-methionine
-
inhibition of D- and L-transamination of D-alanine to 2-oxoglutarate, weak
D-oxamycin
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0.000025 mM, 50% inhibition
D-penicillamine
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1 mM, 73% inhibition
D-serine
-
inhibition of D- and L-transamination of D-alanine to 2-oxoglutarate
DL-alpha-Methylserine
-
inhibition of D- and L-transamination of D-alanine to alpha-ketoglutarate, weak
HgCl2
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0.1 mM, complete inhibition
hydroxylamine
KCl
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80 mM, 50% inhibition
L-cysteine
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2 mM, 49% inhibition
L-oxamycin
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0.001 mM, 50% inhibition
L-Penicillamine
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1 mM, 28% inhibition
L-serine
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10 mM, 22% inhibition
Maleate
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12 mM, 30% inhibition at pH 7.1, no inhibition at pH 8.3
N-ethylmaleimide
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1 mM, 50% inhibition
Na2SO4
-
40 mM, 50% inhibition
NaCl
-
75 mM, 50% inhibition
NH4Cl
-
80 mM, 50% inhibition
oxamycin
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D-isomer by a factor of 40 more inhibitory than L-isomer
p-chloromercuribenzoate
-
4 mM, 36% inhibition, D-alanine and pyridoxal 5'-phosphate protect to some extent
phenylhydrazine
succinate
-
12 mM, 18% inhibition at pH 7.1, no inhibition at pH 8.3
Tris-Cl
-
100 mM, 50% inhibition
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxamine phosphate
-
-
additional information
-
not activated by pyridoxamine
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
14
2-oxobutanoate
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cosubstrate D-alanine
0.06 - 35.6
2-oxoglutarate
15.5 - 32.2
2-oxoisovalerate
1.2 - 20
D-alanine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
260
2-oxoglutarate
Bacillus sp.
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pH 8.5, 50C
0.12 - 340
D-alanine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00225 - 0.01
beta-Chloro-D-alanine
0.000011
D-cycloserine
-
pH 8.0, 37C
0.057
D-penicillamine
-
pH 8.0, 37C
0.8
L-Penicillamine
-
pH 8.0, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.088
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-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.2 - 8.8
9
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80% activity at pH 9
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.5
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optimal activity
8.5 - 9
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
Bacillus sp. (strain YM-1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
53000
-
sedimentation equilibrium centrifugation
58000
-
sedimentation equilibrium centrifugation
65000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallized from solutions containing 0.05 mM pyridoxal 5'-phosphate, 1-2% dioxane, 5 mM sodium azide, 18-22% poly(ethylene glycol) 4000, and 25 mM 2-(N-morpholino)ethanesulfonic acid, pH 5.5-6.5 by the hanging drop method, 1.94 A resolution
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pyridoxal 5'-phosphate and pyridoxamine 5'-phosphate form of L201A mutant enzyme, crystallization from solutions containing 100 mM Tris-HCl, pH 8.5-9.9, 29-33% polyethylenglycol 3350, 300-700 mM sodium acetate, and 5 mM sodium azide by the hanging drop method, crystal structures at 2.0 A resolution
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pyridoxal 5'-phosphate form: hanging drop method, 25% polyethylene glycol 4000, 200 mM ammonium sulfate, 100 mM sodium acetate, pH 4.6 and 1 mM 2-oxoglutarate, single yellow crystals after 2 weeks, enzyme complexed with N-(5'-phosphopyridoxyl)-D-alanine: hanging drop method, 26-28% polyethylene glycol 4000, 300 mM sodium acetate, 100 mM Tris-chloride, pH 8.5, crystal structure at 2.4 and 1.9 A resolution, respectively
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10C, 20 mM potassium phosphate, pH 7.0, 2 months, no loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate, DEAE-Sephadex, partial purification
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DEAE-cellulose, Sephadex G-200, partial purification
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protamine sulfate, ammonium sulfate, DEAE-Sephadex, hydroxylapatite
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recombinant wild-type and mutant enzymes, Resource Q, phenyl-superose
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wild-type, L201A and L201W mutant enzyme, DEAE-toyopearl
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expression of wild-type, L201A and L201W mutant enzymes in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E32A
-
1% of wild-type activity
E32D
-
65% of wild-type activity
E32Q
-
10% of wild-type activity
K33A
-
64% of wild-type activity
L201W
-
0.043% of wild-type kcat
P119G/R120G/P121G
-
higher activity than wild-type with both pyruvate and 2-oxoglutarate as amino acceptors and a variety of D-amino acids except for D-alanine and D-aspartate, reduced thermostability
V33A
-
110% of wild-type activity
Y31A
-
0.4% of wild-type activity
L201A
-
2% of wild-type kcat
-
L201W
-
0.043% of wild-type kcat
-
additional information
-
replacement of the loop core P119-R120-P121 with glycine chains of different lengths: 1, 3, or 5 glycines, mutant forms are much more active than the wild type enzyme in the overall reactions with various amino acids and pyruvate
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