The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics

Biochemistry. 2009 Nov 3;48(43):10467-72. doi: 10.1021/bi9013165.


The enzymes DdaG and DdaF, encoded in the Pantoea agglomerans dapdiamide antibiotic biosynthetic gene cluster, when expressed in Escherichia coli, form the tandem amide bonds of the dapdiamide scaffold at the expense of ATP cleavage. DdaG uses fumarate, 2,3-diaminopropionate (DAP), and ATP to make fumaroyl-AMP transiently on the way to the N(beta)-fumaroyl-DAP regioisomer. Then DdaF acts as a second ATP-dependent amide ligase, but this enzyme cleaves ATP to ADP and P(i) during amide bond formation. However, DdaF will not accept N(beta)-fumaroyl-DAP; the enzyme requires the fumaroyl moiety to be first converted to the fumaramoyl half-amide in N(beta)-fumaramoyl-DAP. DdaF adds Val, Ile, or Leu to the carboxylate of fumaramoyl-DAP to make dapdiamide A, B, or C, respectively. Thus, to build the dapdiamide antibiotic scaffold, amidation must occur on the fumaroyl-DAP scaffold, after DdaG action but before DdaF catalysis. This is an unusual instance of two ligases acting sequentially in untemplated amide bond formations using attack of substrate carboxylates at P(alpha) (AMP-forming) and then at P(gamma) (ADP-forming) of ATP cosubstrates.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Diphosphate / metabolism
  • Adenosine Monophosphate / metabolism
  • Adenosine Triphosphate / metabolism*
  • Anti-Bacterial Agents / biosynthesis*
  • Anti-Bacterial Agents / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Chromatography, High Pressure Liquid
  • Dipeptides / biosynthesis*
  • Dipeptides / chemistry
  • Models, Biological
  • Molecular Structure
  • Pantoea / enzymology*


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Dipeptides
  • Adenosine Monophosphate
  • Adenosine Diphosphate
  • Adenosine Triphosphate