Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases

Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12120-5. doi: 10.1073/pnas.182156699. Epub 2002 Sep 9.


The synthesis of the catecholic siderophore bacillibactin is accomplished by the nonribosomal peptide synthetase (NRPS) encoded by the dhb operon. DhbE is responsible for the initial step in bacillibactin synthesis, the activation of the aryl acid 2,3-dihydroxybenzoate (DHB). The stand-alone adenylation (A) domain DhbE, the structure of which is presented here, exhibits greatest homology to other NRPS A-domains, acyl-CoA ligases and luciferases. It's structure is solved in three different states, without the ligands ATP and DHB (native state), with the product DHB-AMP (adenylate state) and with the hydrolyzed product AMP and DHB (hydrolyzed state). The 59.9-kDa protein folds into two domains, with the active site at the interface between them. In contrast to previous proposals of a major reorientation of the large and small domains on substrate binding, we observe only local structural rearrangements. The structure of the phosphate binding loop could be determined, a motif common to many adenylate-forming enzymes, as well as with bound DHB-adenylate and the hydrolyzed product DHB*AMP. Based on the structure and amino acid sequence alignments, an adapted specificity conferring code for aryl acid activating domains is proposed, allowing assignment of substrate specificity to gene products of previously unknown function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / metabolism
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacillus subtilis / enzymology
  • Bacillus subtilis / genetics
  • Catalytic Domain
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Esters / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Oligopeptides / biosynthesis
  • Oligopeptides / chemistry
  • Peptide Synthases / chemistry*
  • Peptide Synthases / genetics
  • Peptide Synthases / metabolism
  • Protein Conformation
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Homology, Amino Acid
  • Static Electricity
  • Substrate Specificity


  • Esters
  • Oligopeptides
  • Recombinant Proteins
  • bacillibactin
  • Adenosine Monophosphate
  • Peptide Synthases
  • non-ribosomal peptide synthase