7R9X

Crystal structure of a dehydrating condensation domain, AmbE-CmodAA, involved in nonribosomal peptide synthesis

Summary for 7R9X

• Entry DOI: 10.2210/pdb7r9x/pdb
• Descriptor: AmbE, IODIDE ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: condensation domain nonribosomal peptide synthetases (nrpss), biosynthetic protein
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
• Total number of polymer chains: 2
• Total formula weight: 96882.74

Authors

Fortinez, C.M.,Schmeing, T.M. (deposition date: 2021-06-29, release date: 2022-07-13, Last modification date: 2023-10-18)

Primary citation

Patteson, J.B.,Fortinez, C.M.,Putz, A.T.,Rodriguez-Rivas, J.,Bryant 3rd, L.H.,Adhikari, K.,Weigt, M.,Schmeing, T.M.,Li, B.
Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis.
J.Am.Chem.Soc., 144:14057-14070, 2022

PubMed Abstract: Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (C). We also obtain the crystal structure of a C domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-C modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-C identify several key residues for activity, including four residues that are mostly conserved in the C subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for C domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of C domains. Understanding C domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.

PubMed: 35895935
DOI: 10.1021/jacs.1c13404

Experimental method

X-RAY DIFFRACTION (2.14 Å)