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show all sequences of 2.6.99.3

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)
Commentary
Organism
expression in Escherichia coli
Streptomyces lavendulae
Crystallization (Commentary)
Crystallization
Organism
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
Amino acid exchange
Commentary
Organism
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
S121A
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
S121M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
V74T
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
Y97F
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
Y97M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
9
-
Hydroxyurea
wild-type, pH 8.0, 30C
Streptomyces lavendulae
18
-
Hydroxyurea
mutant Y97F, pH 8.0, 30C
Streptomyces lavendulae
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Streptomyces lavendulae
D2Z027
-
-
Streptomyces lavendulae ATCC 11924
D2Z027
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
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
?
-
-
-
-
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
?
-
-
-
-
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae
O-ureido-L-serine + acetate
-
-
-
?
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae ATCC 11924
O-ureido-L-serine + acetate
-
-
-
?
Subunits
Subunits
Commentary
Organism
tetramer
both in solution and in a crystalline state, crystallization data
Streptomyces lavendulae
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.6
-
Hydroxyurea
mutant Y97F, pH 8.0, 30C
Streptomyces lavendulae
11
-
Hydroxyurea
wild-type, pH 8.0, 30C
Streptomyces lavendulae
Cofactor
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
-
Streptomyces lavendulae
Cloned(Commentary) (protein specific)
Commentary
Organism
expression in Escherichia coli
Streptomyces lavendulae
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
-
Streptomyces lavendulae
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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)
Amino acid exchange
Commentary
Organism
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
S121A
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
S121M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
V74T
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
Y97F
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
Y97M
decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine
Streptomyces lavendulae
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
9
-
Hydroxyurea
wild-type, pH 8.0, 30C
Streptomyces lavendulae
18
-
Hydroxyurea
mutant Y97F, pH 8.0, 30C
Streptomyces lavendulae
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
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
?
-
-
-
-
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
?
-
-
-
-
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae
O-ureido-L-serine + acetate
-
-
-
?
O-acetyl-L-serine + hydroxyurea
-
738218
Streptomyces lavendulae ATCC 11924
O-ureido-L-serine + acetate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
tetramer
both in solution and in a crystalline state, crystallization data
Streptomyces lavendulae
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.6
-
Hydroxyurea
mutant Y97F, pH 8.0, 30C
Streptomyces lavendulae
11
-
Hydroxyurea
wild-type, pH 8.0, 30C
Streptomyces lavendulae
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.002
-
Hydroxyurea
mutant S121M, pH 8.0, 30C
Streptomyces lavendulae
0.088
-
Hydroxyurea
mutant Y97M, pH 8.0, 30C
Streptomyces lavendulae
0.094
-
Hydroxyurea
mutant S121A, pH 8.0, 30C
Streptomyces lavendulae
0.22
-
Hydroxyurea
mutant V74T, pH 8.0, 30C
Streptomyces lavendulae
0.25
-
Hydroxyurea
mutant Y97F, pH 8.0, 30C
Streptomyces lavendulae
1.2
-
Hydroxyurea
wild-type, pH 8.0, 30C
Streptomyces lavendulae
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.002
-
Hydroxyurea
mutant S121M, pH 8.0, 30C
Streptomyces lavendulae
0.088
-
Hydroxyurea
mutant Y97M, pH 8.0, 30C
Streptomyces lavendulae
0.094
-
Hydroxyurea
mutant S121A, pH 8.0, 30C
Streptomyces lavendulae
0.22
-
Hydroxyurea
mutant V74T, pH 8.0, 30C
Streptomyces lavendulae
0.25
-
Hydroxyurea
mutant Y97F, pH 8.0, 30C
Streptomyces lavendulae
1.2
-
Hydroxyurea
wild-type, pH 8.0, 30C
Streptomyces lavendulae
Other publictions for EC 2.6.99.3
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
737505
Kumagai
High-level heterologous produc ...
Streptomyces lavendulae, Streptomyces lavendulae ATCC 11924
Appl. Environ. Microbiol.
81
7881-7887
2015
-
1
-
-
-
-
-
-
-
-
-
-
-
5
-
-
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-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
738218
Uda
The structural and mutational ...
Streptomyces lavendulae, Streptomyces lavendulae ATCC 11924
FEBS J.
282
3929-3944
2015
-
-
1
1
6
-
-
2
-
-
-
-
-
6
-
-
-
-
-
-
-
-
4
1
-
-
-
2
-
-
-
1
-
-
-
-
-
1
1
1
6
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
4
1
-
-
-
2
-
-
-
-
-
-
-
-
6
6
721306
Uda
. Establishment of an in vitro ...
Streptomyces lavendulae, Streptomyces lavendulae ATCC 11924
Antimicrob. Agents Chemother.
57
2603-2612
2013
-
-
1
-
-
-
-
1
-
-
2
2
-
6
-
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1
-
-
-
-
-
4
1
1
-
-
1
2
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
-
-
2
2
-
-
-
1
-
-
-
-
4
1
1
-
-
1
2
1
-
-
-
-
-
-
2
2
721300
Kumagai
Molecular cloning and heterolo ...
Streptomyces lavendulae, Streptomyces lavendulae ATCC 11924
Antimicrob. Agents Chemother.
54
1132-1139
2010
-
-
-
-
-
-
-
-
-
-
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2
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5
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-
-
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4
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2
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4
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