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Literature summary extracted from

  • Hollenhorst, M.A.; Clardy, J.; Walsh, C.T.
    The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics (2009), Biochemistry, 48, 10467-10472.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.3.2.B15 expression in Escherichia coli Pantoea agglomerans
6.3.2.46 expression in Escherichia coli Pantoea agglomerans
6.3.2.47 expression in Escherichia coli Pantoea agglomerans

Inhibitors

EC Number Inhibitors Comment Organism Structure
6.3.2.47 Nbeta-fumaramoyl-diaminopropionate substrate inhibition above 0.5 mM Pantoea agglomerans

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
6.3.2.B15 0.26
-
 L-valine pH 8.0, 22°C Pantoea agglomerans
6.3.2.B15 0.83
-
 L-isoleucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.B15 7.82
-
 L-leucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.46 0.55
-
 fumarate pH 8.0, 22°C Pantoea agglomerans
6.3.2.46 20
-
 succinate pH 8.0, 22°C Pantoea agglomerans
6.3.2.47 0.26
-
 L-valine pH 8.0, 22°C Pantoea agglomerans
6.3.2.47 0.83
-
 L-isoleucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.47 7.82
-
 L-leucine pH 8.0, 22°C Pantoea agglomerans

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-isoleucine Pantoea agglomerans the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-isoleucine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-leucine Pantoea agglomerans the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-leucine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-valine Pantoea agglomerans the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-valine
-
 ?
6.3.2.B15 ATP + 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanine + L-valine Pantoea agglomerans the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides ADP + phosphate + 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanyl-L-valine
-
 ?
6.3.2.46 ATP + fumarate + (2S)-2,3-diaminopropionate Pantoea agglomerans the enzyme is involved in biosynthesis of dapdiamide antibiotics (a family of fumaramoyl- and epoxysuccinamoyl-dipeptides, named for the presence of 2,3-diaminopropionate (DAP) and the two amide linkages of the antibiotic scaffold) AMP + diphosphate + (2E)-4-[(2-amino-2-carboxyethyl)amino]-4-oxobut-2-enoate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
6.3.2.B15 Pantoea agglomerans E2JA31
-
-
6.3.2.46 Pantoea agglomerans E2JA32
-
-
6.3.2.47 Pantoea agglomerans E2JA31
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
6.3.2.B15
-
 Pantoea agglomerans
6.3.2.46
-
 Pantoea agglomerans

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-isoleucine
-
 Pantoea agglomerans ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-isoleucine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-isoleucine the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides Pantoea agglomerans ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-isoleucine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-leucine
-
 Pantoea agglomerans ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-leucine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-leucine the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides Pantoea agglomerans ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-leucine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-valine
-
 Pantoea agglomerans ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-valine
-
 ?
6.3.2.B15 ATP + (2E)-4-[[(2S)-2-amino-2-carboxyethyl]amino]-4-oxobut-2-enoate + L-valine the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides Pantoea agglomerans ADP + phosphate + N-[(2S)-3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-2-methylpropanoyl]-L-valine
-
 ?
6.3.2.B15 ATP + 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanine + L-valine
-
 Pantoea agglomerans ADP + phosphate + 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanyl-L-valine
-
 ?
6.3.2.B15 ATP + 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanine + L-valine the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides Pantoea agglomerans ADP + phosphate + 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanyl-L-valine
-
 ?
6.3.2.B15 additional information no activity with Nbeta-fumaroyl-(2S)-2,3-diaminopropionate Pantoea agglomerans ?
-
 ?
6.3.2.46 ATP + fumaramate + (2S)-2,3-diaminopropionate activity with fumaramate is about 15% of the activity compared to fumarate Pantoea agglomerans ?
-
 ?
6.3.2.46 ATP + fumarate + (2S)-2,3-diaminopropionate
-
 Pantoea agglomerans AMP + diphosphate + (2E)-4-[(2-amino-2-carboxyethyl)amino]-4-oxobut-2-enoate
-
 ?
6.3.2.46 ATP + fumarate + (2S)-2,3-diaminopropionate the enzyme is involved in biosynthesis of dapdiamide antibiotics (a family of fumaramoyl- and epoxysuccinamoyl-dipeptides, named for the presence of 2,3-diaminopropionate (DAP) and the two amide linkages of the antibiotic scaffold) Pantoea agglomerans AMP + diphosphate + (2E)-4-[(2-amino-2-carboxyethyl)amino]-4-oxobut-2-enoate
-
 ?
6.3.2.46 ATP + succinate + (2S)-2,3-diaminopropionate activity with succinate is less than 5% of the activity compared to fumarate Pantoea agglomerans ?
-
 ?
6.3.2.46 additional information no activity with the half-amides fumaramate and succinamate succinamate, or with the two enantiomers of trans-epoxysuccinate Pantoea agglomerans ?
-
 ?
6.3.2.47 ATP + 3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-L-alanine + L-isoleucine
-
 Pantoea agglomerans ADP + phosphate + 3-(((2E)-4-amino-4-oxobut-2-enoyl)amino)-L-alanyl-L-isoleucine
-
 ?
6.3.2.47 ATP + 3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-L-alanine + L-leucine
-
 Pantoea agglomerans ADP + phosphate + 3-(((2E)-4-amino-4-oxobut-2-enoyl)amino)-L-alanyl-L-leucine
-
 ?
6.3.2.47 ATP + 3-[[(2E)-4-amino-4-oxobut-2-enoyl]amino]-L-alanine + L-valine
-
 Pantoea agglomerans ADP + phosphate + 3-(((2E)-4-amino-4-oxobut-2-enoyl)amino)-L-alanyl-L-valine
-
 ?
6.3.2.47 additional information DdaF will not accept Nbeta-fumaroyl-diaminopropionate or Nalpha-fumaramoyl-diaminopropionate. The enzyme requires the fumaroyl moiety to be first converted to the fumaramoyl half amide in Nbeta-fumaramoyl-diaminopropionate Pantoea agglomerans ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
6.3.2.B15 DdaF
-
 Pantoea agglomerans
6.3.2.46 DdaG
-
 Pantoea agglomerans
6.3.2.46 fumaroyl-2,3-diaminopropionate ligase
-
 Pantoea agglomerans
6.3.2.47 DdaF
-
 Pantoea agglomerans

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
6.3.2.B15 22
-
 assay at Pantoea agglomerans
6.3.2.46 22
-
 assay at Pantoea agglomerans

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
6.3.2.B15 0.135
-
 L-valine pH 8.0, 22°C Pantoea agglomerans
6.3.2.B15 0.16
-
 L-isoleucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.B15 0.19
-
 L-leucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.46 3.8
-
 succinate pH 8.0, 22°C Pantoea agglomerans
6.3.2.46 11.6
-
 fumarate pH 8.0, 22°C Pantoea agglomerans

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.3.2.B15 8
-
 assay at Pantoea agglomerans
6.3.2.46 8
-
 assay at Pantoea agglomerans

General Information

EC Number General Information Comment Organism
6.3.2.B15 physiological function the enzyme is involved in biosynthesis of fumaramoyl- and epoxysuccinamoyl-dipeptides Pantoea agglomerans
6.3.2.46 physiological function the enzyme is involved in biosynthesis of dapdiamide antibiotics (a family of fumaramoyl- and epoxysuccinamoyl-dipeptides, named for the presence of 2,3-diaminopropionate (DAP) and the two amide linkages of the antibiotic scaffold) Pantoea agglomerans
6.3.2.47 physiological function gene DdaF belongs to the dapdiamide antibiotic biosynthetic gene cluster. DdaF acts as a second ATP-dependent amide ligase, cleaving ATP to ADP and Pi during amide bond formation. DdaF adds Val, Ile, or Leu to the carboxylate of fumaramoyl-2,3-diaminopropionate to make the three dapdiamides A-C. To build the dapdiamide antibiotic scaffold, amidation must occur on the fumaroyl-diaminopropionate scaffold, after DdaG action but before DdaF catalysis Pantoea agglomerans

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
6.3.2.B15 0.024
-
 L-leucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.B15 0.19
-
 L-isoleucine pH 8.0, 22°C Pantoea agglomerans
6.3.2.B15 0.52
-
 L-valine pH 8.0, 22°C Pantoea agglomerans
6.3.2.46 0.19
-
 succinate pH 8.0, 22°C Pantoea agglomerans
6.3.2.46 21
-
 fumarate pH 8.0, 22°C Pantoea agglomerans