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Literature summary for 6.3.2.49 extracted from

  • Shomura, Y.; Hinokuchi, E.; Ikeda, H.; Senoo, A.; Takahashi, Y.; Saito, J.; Komori, H.; Shibata, N.; Yonetani, Y.; Higuchi, Y.
    Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis (2012), Protein Sci., 21, 707-716.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 6.3.2.49

Application

Application Comment Organism
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)

Cloned (Comment) Organism
-
 Bacillus subtilis

Crystallization (Commentary)

Crystallization (Comment) Organism
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 20°C Bacillus subtilis

Protein Variants

Protein Variants Comment Organism
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
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

Inhibitors Comment Organism Structure
(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]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.5
-
 L-alanine pH 7.1, 37°C, mutant enzyme Y75F Bacillus subtilis
1.7
-
 L-alanine pH 7.7, 37°C, mutant enzyme Y75F Bacillus subtilis
2
-
 L-alanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
2.6
-
 L-alanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
4.6
-
 L-alanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis
4.9
-
 L-alanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
16
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis
18
-
 L-phenylalanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
38
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
44
-
 L-phenylalanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
45
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme Bacillus subtilis
92
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme Bacillus subtilis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 ?
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

Organism UniProt Comment Textmining
Bacillus subtilis P39641
-
-
Bacillus subtilis 168 P39641
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Bacillus subtilis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(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 Bacillus subtilis (2S)-3-[(3)-[(1R)-1-aminoethyl(phosphonooxy)]phosphoryl]-2-benzylpropanoic acid + ADP
-
 ?
(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 Bacillus subtilis 168 (2S)-3-[(3)-[(1R)-1-aminoethyl(phosphonooxy)]phosphoryl]-2-benzylpropanoic acid + ADP
-
 ?
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 ?
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 ?
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 Bacillus subtilis ADP + phosphate + L-alanyl-L-phenylalanine
-
 ?
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 Bacillus subtilis 168 ADP + phosphate + L-alanyl-L-phenylalanine
-
 ?

Subunits

Subunits Comment Organism
monomer
-
 Bacillus subtilis

Synonyms

Synonyms Comment Organism
BacD
-
 Bacillus subtilis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Bacillus subtilis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
7.2
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme Bacillus subtilis
7.2
-
 L-alanine pH 7.1, 37°C, mutant enzyme Y75F Bacillus subtilis
7.7
-
 L-alanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
7.7
-
 L-phenylalanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
7.8
-
 L-alanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
7.8
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
9.7
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme Bacillus subtilis
9.7
-
 L-alanine pH 7.7, 37°C, mutant enzyme Y75F Bacillus subtilis
9.7
-
 L-alanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
9.7
-
 L-phenylalanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
10.8
-
 L-alanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis
10.8
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.7
-
 assay at Bacillus subtilis

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.0154
-
 (2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid pH 7.7, 37°C Bacillus subtilis