The Thioesterase Domain of the Fengycin Biosynthesis Cluster: A Structural Base for the Macrocyclization of a Non-ribosomal Lipopeptide

• Published in: Journal of molecular biology 2006-06, Vol.359 (4), p.876-889
• Main Authors: Samel, Stefan A., Wagner, Björn, Marahiel, Mohamed A., Essen, Lars-Oliver
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacillus subtilis; Bacillus subtilis - enzymology; Bacillus subtilis - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; Catalytic Domain; catalytic triad; Crystallography, X-Ray; fengycin; Lipopeptides; Lipoproteins - biosynthesis; macrocyclization; Models, Molecular; Molecular Sequence Data; non-ribosomal peptide synthesis; Peptide Biosynthesis, Nucleic Acid-Independent; Peptide Synthases - antagonists & inhibitors; Peptide Synthases - chemistry; Peptide Synthases - metabolism; Peptides, Cyclic - chemistry; Peptides, Cyclic - metabolism; Phenylmethylsulfonyl Fluoride - chemistry; Phenylmethylsulfonyl Fluoride - metabolism; Protein Conformation; Protein Structure, Tertiary; Ribosomal Proteins - chemistry; Ribosomal Proteins - metabolism; Sequence Homology, Amino Acid; Structural Homology, Protein; thioesterase structure; Thiolester Hydrolases - chemistry; Thiolester Hydrolases - metabolism
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2006.03.062

Many secondary metabolic peptides from bacteria and fungi are produced by non-ribosomal peptide synthetases (NRPS) where the final step of biosynthesis is often catalysed by designated thioesterase domains. Here, we report the 1.8 Å crystal structure of the fengycin thioesterase (FenTE) from Bacillus subtilis F29-3, which catalyses the regio- and stereoselective release and macrocyclization of the antibiotic fengycin from the NRPS template. A structure of the PMSF-inactivated FenTE domain suggests the location of the oxyanion hole and the binding site of the C-terminal residue l-Ile11 of the lipopeptide. Using a combination of docking, molecular dynamics simulations and in vitro activity assays, a model of the FenTE–fengycin complex was derived in which peptide cyclization requires strategic interactions with residues lining the active site canyon.