BRENDA - Enzyme Database

The structural and mutational analyses of O-ureido-L-serine synthase necessary for D-cycloserine biosynthesis

Uda, N.; Matoba, Y.; Oda, K.; Kumagai, T.; Sugiyama, M.; FEBS J. 282, 3929-3944 (2015)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
2.5.1.47
expression in Escherichia coli
Streptomyces lavendulae
2.6.99.3
expression in Escherichia coli
Streptomyces lavendulae
Crystallization (Commentary)
EC Number
Crystallization
Organism
2.5.1.47
wild-type and mutant K43A, to 2.25 and 1.9 A resolution, respectively. Each monomer of DcsD takes a typical fold of type II pyridoxal 5'-phosphate enzymes with the cofactor pyridoxal 5'-phosphate covalently bound to invariant Lys residue (Lys43) at the active site. The pyridine ring of pyridoxal 5'-phoshate makes hydrogen bonds with invariant Asn73 and Ser265 residues. Its phosphate group makes hydrogen bonds with Gly177, Thr178, Thr179 and Thr181 residues
Streptomyces lavendulae
2.6.99.3
wild-type and mutant K43A, to 2.25 and 1.9 A resolution, respectively. Each monomer of DcsD takes a typical fold of type II pyridoxal 5'-phosphate enzymes with the cofactor pyridoxal 5'-phosphate covalently bound to invariant Lys residue (Lys43) at the active site. The pyridine ring of pyridoxal 5'-phoshate makes hydrogen bonds with invariant Asn73 and Ser265 residues. Its phosphate group makes hydrogen bonds with Gly177, Thr178, Thr179 and Thr181 residues
Streptomyces lavendulae
Engineering
EC Number
Amino acid exchange
Commentary
Organism
2.5.1.47
K43A
mutation in invariant Lys43 residue, inactive. Mutant forms an external aldimine adduct upon addition of L-methionine or O-ureido-L-serine
Streptomyces lavendulae
2.5.1.47
S121A
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
S121M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
V74T
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
Y97F
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
Y97M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
K43A
mutation in invariant Lys43 residue, inactive. Mutant forms an external aldimine adduct upon addition of L-methionine or O-ureido-L-serine
Streptomyces lavendulae
2.6.99.3
S121A
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
S121M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
V74T
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
Y97F
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
Y97M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.5.1.47
0.073
-
H2S
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.084
-
H2S
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.095
-
H2S
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.12
-
H2S
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.14
-
H2S
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.2
-
H2S
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
9
-
Hydroxyurea
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
18
-
Hydroxyurea
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
2.5.1.47
Streptomyces lavendulae
D2Z027
-
-
2.5.1.47
Streptomyces lavendulae ATCC 11924
D2Z027
-
-
2.6.99.3
Streptomyces lavendulae
D2Z027
-
-
2.6.99.3
Streptomyces lavendulae ATCC 11924
D2Z027
-
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.5.1.47
additional information
enzyme additionally catalyzes the formation of O-ureido-L-serine from O-acetyl-L-serine and hydroxyurea, reaction of EC 2.6.99.3. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae
?
-
-
-
-
2.5.1.47
additional information
enzyme additionally catalyzes the formation of O-ureido-L-serine from O-acetyl-L-serine and hydroxyurea, reaction of EC 2.6.99.3. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae ATCC 11924
?
-
-
-
-
2.5.1.47
o-acetyl-L-serine + H2S
-
738218
Streptomyces lavendulae
L-cysteine + acetate
-
-
-
?
2.5.1.47
o-acetyl-L-serine + H2S
-
738218
Streptomyces lavendulae ATCC 11924
L-cysteine + acetate
-
-
-
?
2.6.99.3
additional information
enzyme additionally catalyzes the formation of L-cysteine from O-acetyl-L-serine and H2S, reaction of EC 2.5.1.47. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae
?
-
-
-
-
2.6.99.3
additional information
enzyme additionally catalyzes the formation of L-cysteine from O-acetyl-L-serine and H2S, reaction of EC 2.5.1.47. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae ATCC 11924
?
-
-
-
-
2.6.99.3
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae
O-ureido-L-serine + acetate
-
-
-
?
2.6.99.3
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae ATCC 11924
O-ureido-L-serine + acetate
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
2.5.1.47
tetramer
both in solution and in a crystalline state, crystallization data
Streptomyces lavendulae
2.6.99.3
tetramer
both in solution and in a crystalline state, crystallization data
Streptomyces lavendulae
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.5.1.47
10
-
H2S
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
12
-
H2S
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
15
-
H2S
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
22
-
H2S
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
26
-
H2S
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
44
-
H2S
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
4.6
-
Hydroxyurea
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
11
-
Hydroxyurea
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
2.5.1.47
pyridoxal 5'-phosphate
-
Streptomyces lavendulae
2.6.99.3
pyridoxal 5'-phosphate
-
Streptomyces lavendulae
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
2.5.1.47
expression in Escherichia coli
Streptomyces lavendulae
2.6.99.3
expression in Escherichia coli
Streptomyces lavendulae
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
2.5.1.47
pyridoxal 5'-phosphate
-
Streptomyces lavendulae
2.6.99.3
pyridoxal 5'-phosphate
-
Streptomyces lavendulae
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
2.5.1.47
wild-type and mutant K43A, to 2.25 and 1.9 A resolution, respectively. Each monomer of DcsD takes a typical fold of type II pyridoxal 5'-phosphate enzymes with the cofactor pyridoxal 5'-phosphate covalently bound to invariant Lys residue (Lys43) at the active site. The pyridine ring of pyridoxal 5'-phoshate makes hydrogen bonds with invariant Asn73 and Ser265 residues. Its phosphate group makes hydrogen bonds with Gly177, Thr178, Thr179 and Thr181 residues
Streptomyces lavendulae
2.6.99.3
wild-type and mutant K43A, to 2.25 and 1.9 A resolution, respectively. Each monomer of DcsD takes a typical fold of type II pyridoxal 5'-phosphate enzymes with the cofactor pyridoxal 5'-phosphate covalently bound to invariant Lys residue (Lys43) at the active site. The pyridine ring of pyridoxal 5'-phoshate makes hydrogen bonds with invariant Asn73 and Ser265 residues. Its phosphate group makes hydrogen bonds with Gly177, Thr178, Thr179 and Thr181 residues
Streptomyces lavendulae
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
2.5.1.47
K43A
mutation in invariant Lys43 residue, inactive. Mutant forms an external aldimine adduct upon addition of L-methionine or O-ureido-L-serine
Streptomyces lavendulae
2.5.1.47
S121A
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
S121M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
V74T
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
Y97F
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.5.1.47
Y97M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
K43A
mutation in invariant Lys43 residue, inactive. Mutant forms an external aldimine adduct upon addition of L-methionine or O-ureido-L-serine
Streptomyces lavendulae
2.6.99.3
S121A
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
S121M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
V74T
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
Y97F
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
2.6.99.3
Y97M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.5.1.47
0.073
-
H2S
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.084
-
H2S
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.095
-
H2S
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.12
-
H2S
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.14
-
H2S
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
0.2
-
H2S
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
9
-
Hydroxyurea
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
18
-
Hydroxyurea
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.5.1.47
additional information
enzyme additionally catalyzes the formation of O-ureido-L-serine from O-acetyl-L-serine and hydroxyurea, reaction of EC 2.6.99.3. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae
?
-
-
-
-
2.5.1.47
additional information
enzyme additionally catalyzes the formation of O-ureido-L-serine from O-acetyl-L-serine and hydroxyurea, reaction of EC 2.6.99.3. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae ATCC 11924
?
-
-
-
-
2.5.1.47
o-acetyl-L-serine + H2S
-
738218
Streptomyces lavendulae
L-cysteine + acetate
-
-
-
?
2.5.1.47
o-acetyl-L-serine + H2S
-
738218
Streptomyces lavendulae ATCC 11924
L-cysteine + acetate
-
-
-
?
2.6.99.3
additional information
enzyme additionally catalyzes the formation of L-cysteine from O-acetyl-L-serine and H2S, reaction of EC 2.5.1.47. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae
?
-
-
-
-
2.6.99.3
additional information
enzyme additionally catalyzes the formation of L-cysteine from O-acetyl-L-serine and H2S, reaction of EC 2.5.1.47. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis
738218
Streptomyces lavendulae ATCC 11924
?
-
-
-
-
2.6.99.3
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae
O-ureido-L-serine + acetate
-
-
-
?
2.6.99.3
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae ATCC 11924
O-ureido-L-serine + acetate
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
2.5.1.47
tetramer
both in solution and in a crystalline state, crystallization data
Streptomyces lavendulae
2.6.99.3
tetramer
both in solution and in a crystalline state, crystallization data
Streptomyces lavendulae
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.5.1.47
10
-
H2S
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
12
-
H2S
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
15
-
H2S
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
22
-
H2S
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
26
-
H2S
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
44
-
H2S
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
4.6
-
Hydroxyurea
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
11
-
Hydroxyurea
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
2.5.1.47
100
-
H2S
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
140
-
H2S
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
160
-
H2S
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
190
-
H2S
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
220
-
H2S
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
260
-
H2S
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.002
-
Hydroxyurea
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.088
-
Hydroxyurea
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.094
-
Hydroxyurea
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.22
-
Hydroxyurea
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.25
-
Hydroxyurea
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
1.2
-
Hydroxyurea
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
2.5.1.47
100
-
H2S
wild-type, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
140
-
H2S
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
160
-
H2S
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
190
-
H2S
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
220
-
H2S
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.5.1.47
260
-
H2S
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.002
-
Hydroxyurea
mutant S121M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.088
-
Hydroxyurea
mutant Y97M, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.094
-
Hydroxyurea
mutant S121A, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.22
-
Hydroxyurea
mutant V74T, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
0.25
-
Hydroxyurea
mutant Y97F, pH 8.0, 30°C
Streptomyces lavendulae
2.6.99.3
1.2
-
Hydroxyurea
wild-type, pH 8.0, 30°C
Streptomyces lavendulae