BRENDA - Enzyme Database

Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis

Shomura, Y.; Hinokuchi, E.; Ikeda, H.; Senoo, A.; Takahashi, Y.; Saito, J.; Komori, H.; Shibata, N.; Yonetani, Y.; Higuchi, Y.; Protein Sci. 21, 707-716 (2012)

Data extracted from this reference:

Application
EC Number
Application
Commentary
Organism
6.3.2.49
pharmacology
potential application in industrial protein engineering for the environmentally friendly biological production of useful peptide compounds, such as physiologically active peptides, artificial sweeteners and antibiotics
Bacillus subtilis
Cloned(Commentary)
EC Number
Cloned (Commentary)
Organism
6.3.2.49
-
Bacillus subtilis
Crystallization (Commentary)
EC Number
Crystallization (Commentary)
Organism
6.3.2.49
crystal structure of the enzyme in complex with ADP and an intermediate analog, phosphorylated phosphinate L-alanyl-L-phenylalanine, refined to 2.5 A resolution, sitting-drop vapor-diffusion method at 20C
Bacillus subtilis
Engineering
EC Number
Protein Variants
Commentary
Organism
6.3.2.49
S1845A
no significant difference in kcat value between the wild type and the mutant enzyme. 2fold increase in Km-value for L-alanine
Bacillus subtilis
6.3.2.49
Y75F
no significant difference in kcat value between the wild type and the mutant enzyme, 2fold increase in KM-value for L-phenylalanine
Bacillus subtilis
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
6.3.2.49
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid
competitive inhibition for L-alanine but not for L-phenylalanine
Bacillus subtilis
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
6.3.2.49
1.5
-
L-alanine
pH 7.1, 37C, mutant enzyme Y75F
Bacillus subtilis
6.3.2.49
1.7
-
L-alanine
pH 7.7, 37C, mutant enzyme Y75F
Bacillus subtilis
6.3.2.49
2
-
L-alanine
pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
2.6
-
L-alanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
4.6
-
L-alanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
6.3.2.49
4.9
-
L-alanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
16
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
6.3.2.49
18
-
L-phenylalanine
pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
38
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
44
-
L-phenylalanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
45
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme
Bacillus subtilis
6.3.2.49
92
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme
Bacillus subtilis
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
Bacillus subtilis
-
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
?
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
Bacillus subtilis 168
-
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
?
Organism
EC Number
Organism
UniProt
Commentary
Textmining
6.3.2.49
Bacillus subtilis
P39641
-
-
6.3.2.49
Bacillus subtilis 168
P39641
-
-
Purification (Commentary)
EC Number
Purification (Commentary)
Organism
6.3.2.49
-
Bacillus subtilis
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
6.3.2.49
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid + ATP
the phosphinate L-alanyl-L-phenylalanine analog binds the active site of the enzyme, and accepts a phosphate group from ATP to form the phosphorylated phosphinate L-alanyl-L-phenylalanine analog
730896
Bacillus subtilis
(2S)-3-[(3)-[(1R)-1-aminoethyl(phosphonooxy)]phosphoryl]-2-benzylpropanoic acid + ADP
-
-
-
?
6.3.2.49
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid + ATP
the phosphinate L-alanyl-L-phenylalanine analog binds the active site of the enzyme, and accepts a phosphate group from ATP to form the phosphorylated phosphinate L-alanyl-L-phenylalanine analog
730896
Bacillus subtilis 168
(2S)-3-[(3)-[(1R)-1-aminoethyl(phosphonooxy)]phosphoryl]-2-benzylpropanoic acid + ADP
-
-
-
?
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
-
730896
Bacillus subtilis
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
-
?
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
-
730896
Bacillus subtilis 168
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
-
?
6.3.2.49
ATP + L-alanine + L-phenylalanine
the substrate pair L-alanine and L-phenylalanine shows the highest activity among the combinations of less bulky amino acids (glycine, L-alanine, and L-serine) and uncharged bulky amino acids (L-leucine, L-isolucine, L-methionine, L-phenylalanine, L-tyrosine, L-tryptophane, and L-glutamine). Some D-amino acids (D-alanine, D-serine, D-phenylalanine, and D-glutamine) are tested but show no activity
730896
Bacillus subtilis
ADP + phosphate + L-alanyl-L-phenylalanine
-
-
-
?
6.3.2.49
ATP + L-alanine + L-phenylalanine
the substrate pair L-alanine and L-phenylalanine shows the highest activity among the combinations of less bulky amino acids (glycine, L-alanine, and L-serine) and uncharged bulky amino acids (L-leucine, L-isolucine, L-methionine, L-phenylalanine, L-tyrosine, L-tryptophane, and L-glutamine). Some D-amino acids (D-alanine, D-serine, D-phenylalanine, and D-glutamine) are tested but show no activity
730896
Bacillus subtilis 168
ADP + phosphate + L-alanyl-L-phenylalanine
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
6.3.2.49
monomer
-
Bacillus subtilis
Synonyms
EC Number
Synonyms
Commentary
Organism
6.3.2.49
BacD
-
Bacillus subtilis
Temperature Optimum [C]
EC Number
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
6.3.2.49
37
-
assay at
Bacillus subtilis
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
6.3.2.49
7.2
-
L-alanine
pH 7.1, 37C, mutant enzyme Y75F
Bacillus subtilis
6.3.2.49
7.2
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme
Bacillus subtilis
6.3.2.49
7.7
-
L-alanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
7.7
-
L-phenylalanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
7.8
-
L-alanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
7.8
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
9.7
-
L-alanine
pH 7.7, 37C, mutant enzyme Y75F; pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
9.7
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme; pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
10.8
-
L-alanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
6.3.2.49
10.8
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
6.3.2.49
7.7
-
assay at
Bacillus subtilis
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
6.3.2.49
0.0154
-
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid
pH 7.7, 37C
Bacillus subtilis
Application (protein specific)
EC Number
Application
Commentary
Organism
6.3.2.49
pharmacology
potential application in industrial protein engineering for the environmentally friendly biological production of useful peptide compounds, such as physiologically active peptides, artificial sweeteners and antibiotics
Bacillus subtilis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
6.3.2.49
-
Bacillus subtilis
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
6.3.2.49
crystal structure of the enzyme in complex with ADP and an intermediate analog, phosphorylated phosphinate L-alanyl-L-phenylalanine, refined to 2.5 A resolution, sitting-drop vapor-diffusion method at 20C
Bacillus subtilis
Engineering (protein specific)
EC Number
Protein Variants
Commentary
Organism
6.3.2.49
S1845A
no significant difference in kcat value between the wild type and the mutant enzyme. 2fold increase in Km-value for L-alanine
Bacillus subtilis
6.3.2.49
Y75F
no significant difference in kcat value between the wild type and the mutant enzyme, 2fold increase in KM-value for L-phenylalanine
Bacillus subtilis
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
6.3.2.49
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid
competitive inhibition for L-alanine but not for L-phenylalanine
Bacillus subtilis
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
6.3.2.49
0.0154
-
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid
pH 7.7, 37C
Bacillus subtilis
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
6.3.2.49
1.5
-
L-alanine
pH 7.1, 37C, mutant enzyme Y75F
Bacillus subtilis
6.3.2.49
1.7
-
L-alanine
pH 7.7, 37C, mutant enzyme Y75F
Bacillus subtilis
6.3.2.49
2
-
L-alanine
pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
2.6
-
L-alanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
4.6
-
L-alanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
6.3.2.49
4.9
-
L-alanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
16
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
6.3.2.49
18
-
L-phenylalanine
pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
38
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
44
-
L-phenylalanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
45
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme
Bacillus subtilis
6.3.2.49
92
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme
Bacillus subtilis
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
Bacillus subtilis
-
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
?
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
Bacillus subtilis 168
-
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
6.3.2.49
-
Bacillus subtilis
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
6.3.2.49
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid + ATP
the phosphinate L-alanyl-L-phenylalanine analog binds the active site of the enzyme, and accepts a phosphate group from ATP to form the phosphorylated phosphinate L-alanyl-L-phenylalanine analog
730896
Bacillus subtilis
(2S)-3-[(3)-[(1R)-1-aminoethyl(phosphonooxy)]phosphoryl]-2-benzylpropanoic acid + ADP
-
-
-
?
6.3.2.49
(2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid + ATP
the phosphinate L-alanyl-L-phenylalanine analog binds the active site of the enzyme, and accepts a phosphate group from ATP to form the phosphorylated phosphinate L-alanyl-L-phenylalanine analog
730896
Bacillus subtilis 168
(2S)-3-[(3)-[(1R)-1-aminoethyl(phosphonooxy)]phosphoryl]-2-benzylpropanoic acid + ADP
-
-
-
?
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
-
730896
Bacillus subtilis
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
-
?
6.3.2.49
ATP + L-alanine + (1R,2S,6R)-anticapsin
-
730896
Bacillus subtilis 168
ADP + phosphate + bacilysin
bacilysin i.e. L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
-
-
?
6.3.2.49
ATP + L-alanine + L-phenylalanine
the substrate pair L-alanine and L-phenylalanine shows the highest activity among the combinations of less bulky amino acids (glycine, L-alanine, and L-serine) and uncharged bulky amino acids (L-leucine, L-isolucine, L-methionine, L-phenylalanine, L-tyrosine, L-tryptophane, and L-glutamine). Some D-amino acids (D-alanine, D-serine, D-phenylalanine, and D-glutamine) are tested but show no activity
730896
Bacillus subtilis
ADP + phosphate + L-alanyl-L-phenylalanine
-
-
-
?
6.3.2.49
ATP + L-alanine + L-phenylalanine
the substrate pair L-alanine and L-phenylalanine shows the highest activity among the combinations of less bulky amino acids (glycine, L-alanine, and L-serine) and uncharged bulky amino acids (L-leucine, L-isolucine, L-methionine, L-phenylalanine, L-tyrosine, L-tryptophane, and L-glutamine). Some D-amino acids (D-alanine, D-serine, D-phenylalanine, and D-glutamine) are tested but show no activity
730896
Bacillus subtilis 168
ADP + phosphate + L-alanyl-L-phenylalanine
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
6.3.2.49
monomer
-
Bacillus subtilis
Temperature Optimum [C] (protein specific)
EC Number
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
6.3.2.49
37
-
assay at
Bacillus subtilis
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
6.3.2.49
7.2
-
L-alanine
pH 7.1, 37C, mutant enzyme Y75F
Bacillus subtilis
6.3.2.49
7.2
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme
Bacillus subtilis
6.3.2.49
7.7
-
L-alanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
7.7
-
L-phenylalanine
pH 7.1, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
7.8
-
L-alanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
7.8
-
L-phenylalanine
pH 7.1, 37C, mutant enzyme S184F
Bacillus subtilis
6.3.2.49
9.7
-
L-alanine
pH 7.7, 37C, mutant enzyme Y75F; pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
9.7
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme; pH 7.7, 37C, wild-type enzyme
Bacillus subtilis
6.3.2.49
10.8
-
L-alanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
6.3.2.49
10.8
-
L-phenylalanine
pH 7.7, 37C, mutant enzyme S184A
Bacillus subtilis
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
6.3.2.49
7.7
-
assay at
Bacillus subtilis