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Title: Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions

Abstract

Nonribosomal peptide synthetases (NRPSs) underlie the biosynthesis of many natural products that have important medicinal utility. Protection of the NRPS peptide products from proteolysis is critical to these pathways and is often achieved by structural modification, principally the introduction of D-amino acid residues into the elongating peptide. These amino acids are generally formed in situ from their L-stereoisomers by epimerization domains or dual-function condensation/epimerization domains. In singular contrast, the thioesterase domain of nocardicin biosynthesis mediates both the effectively complete L- to D-epimerization of its C-terminal amino acid residue (≥100:1) and hydrolytic product release. We report herein high-resolution crystal structures of the nocardicin thioesterase domain in ligand-free form and reacted with a structurally precise fluorophosphonate substrate mimic that identify the complete peptide binding pocket to accommodate both stereoisomers. These structures combined with additional functional studies provide detailed mechanistic insight into this unique dual-function NRPS domain.

Authors:
ORCiD logo [1];  [2];  [2];  [2]; ORCiD logo [2]; ORCiD logo [1]
  1. State Univ. of New York (SUNY), Buffalo, NY (United States)
  2. Johns Hopkins Univ., Baltimore, MD (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source
Sponsoring Org.:
National Institutes of Health (NIH); National Cancer Institute (NCI); National Institute of General Medical Sciences (NIGMS); USDOE Office of Science (SC)
OSTI Identifier:
1599428
Grant/Contract Number:  
AI121072; GM116957; AC02-06CH11357; AC02-98CH10886
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biosynthesis; Enzyme mechanisms; X-ray crystallography

Citation Formats

Patel, Ketan D., d’Andrea, Felipe B., Gaudelli, Nicole M., Buller, Andrew R., Townsend, Craig A., and Gulick, Andrew M. Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions. United States: N. p., 2019. Web. https://doi.org/10.1038/s41467-019-11740-6.
Patel, Ketan D., d’Andrea, Felipe B., Gaudelli, Nicole M., Buller, Andrew R., Townsend, Craig A., & Gulick, Andrew M. Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions. United States. https://doi.org/10.1038/s41467-019-11740-6
Patel, Ketan D., d’Andrea, Felipe B., Gaudelli, Nicole M., Buller, Andrew R., Townsend, Craig A., and Gulick, Andrew M. Tue . "Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions". United States. https://doi.org/10.1038/s41467-019-11740-6. https://www.osti.gov/servlets/purl/1599428.
@article{osti_1599428,
title = {Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions},
author = {Patel, Ketan D. and d’Andrea, Felipe B. and Gaudelli, Nicole M. and Buller, Andrew R. and Townsend, Craig A. and Gulick, Andrew M.},
abstractNote = {Nonribosomal peptide synthetases (NRPSs) underlie the biosynthesis of many natural products that have important medicinal utility. Protection of the NRPS peptide products from proteolysis is critical to these pathways and is often achieved by structural modification, principally the introduction of D-amino acid residues into the elongating peptide. These amino acids are generally formed in situ from their L-stereoisomers by epimerization domains or dual-function condensation/epimerization domains. In singular contrast, the thioesterase domain of nocardicin biosynthesis mediates both the effectively complete L- to D-epimerization of its C-terminal amino acid residue (≥100:1) and hydrolytic product release. We report herein high-resolution crystal structures of the nocardicin thioesterase domain in ligand-free form and reacted with a structurally precise fluorophosphonate substrate mimic that identify the complete peptide binding pocket to accommodate both stereoisomers. These structures combined with additional functional studies provide detailed mechanistic insight into this unique dual-function NRPS domain.},
doi = {10.1038/s41467-019-11740-6},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {8}
}

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