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Literature summary 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

Application

EC Number Application Comment 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 (Comment) Organism
6.3.2.49
-
 Bacillus subtilis

Crystallization (Commentary)

EC Number Crystallization (Comment) 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 20°C Bacillus subtilis

Protein Variants

EC Number Protein Variants Comment 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 Comment 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 Comment Organism Structure
6.3.2.49 1.5
-
 L-alanine pH 7.1, 37°C, mutant enzyme Y75F Bacillus subtilis
6.3.2.49 1.7
-
 L-alanine pH 7.7, 37°C, mutant enzyme Y75F Bacillus subtilis
6.3.2.49 2
-
 L-alanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 2.6
-
 L-alanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 4.6
-
 L-alanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis
6.3.2.49 4.9
-
 L-alanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
6.3.2.49 16
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis
6.3.2.49 18
-
 L-phenylalanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 38
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
6.3.2.49 44
-
 L-phenylalanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 45
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme Bacillus subtilis
6.3.2.49 92
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme Bacillus subtilis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 Comment Textmining
6.3.2.49 Bacillus subtilis P39641
-
-
6.3.2.49 Bacillus subtilis 168 P39641
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
6.3.2.49
-
 Bacillus subtilis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 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 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
-
 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 ?
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 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 Bacillus subtilis 168 ADP + phosphate + L-alanyl-L-phenylalanine
-
 ?

Subunits

EC Number Subunits Comment Organism
6.3.2.49 monomer
-
 Bacillus subtilis

Synonyms

EC Number Synonyms Comment Organism
6.3.2.49 BacD
-
 Bacillus subtilis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment 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 Comment Organism Structure
6.3.2.49 7.2
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme Bacillus subtilis
6.3.2.49 7.2
-
 L-alanine pH 7.1, 37°C, mutant enzyme Y75F Bacillus subtilis
6.3.2.49 7.7
-
 L-alanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 7.7
-
 L-phenylalanine pH 7.1, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 7.8
-
 L-alanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
6.3.2.49 7.8
-
 L-phenylalanine pH 7.1, 37°C, mutant enzyme S184F Bacillus subtilis
6.3.2.49 9.7
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme Bacillus subtilis
6.3.2.49 9.7
-
 L-alanine pH 7.7, 37°C, mutant enzyme Y75F Bacillus subtilis
6.3.2.49 9.7
-
 L-alanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 9.7
-
 L-phenylalanine pH 7.7, 37°C, wild-type enzyme Bacillus subtilis
6.3.2.49 10.8
-
 L-alanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis
6.3.2.49 10.8
-
 L-phenylalanine pH 7.7, 37°C, mutant enzyme S184A Bacillus subtilis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.3.2.49 7.7
-
 assay at Bacillus subtilis

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
6.3.2.49 0.0154
-
 (2S)-3-[[(1R)-1-aminoethyl(hydroxy)]phosphoryl]-2-benzylpropionic acid pH 7.7, 37°C Bacillus subtilis