Structure and Function of NzeB, a Versatile C–C and C–N Bond-Forming Diketopiperazine Dimerase
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nihms-1620549.pdf
Description
Accepted version
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3.63 MB
Format
Adobe PDF
Checksum (MD5)
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Author(s)
Shende, Vikram V
Khatri, Yogan
Newmister, Sean A
Sanders, Jacob N
Lindovska, Petra
Yu, Fengan
Doyon, Tyler J
Kim, Justin
Houk, KN
Movassaghi, Mohammad
Date Issued
2020
Journal
Journal of the American Chemical Society
Publisher
American Chemical Society (ACS)
Citation
Shende, Vikram V, Khatri, Yogan, Newmister, Sean A, Sanders, Jacob N, Lindovska, Petra et al. 2020. "Structure and Function of NzeB, a Versatile C–C and C–N Bond-Forming Diketopiperazine Dimerase." Journal of the American Chemical Society, 142 (41).
Version
Author's final manuscript
Abstract
© 2020 American Chemical Society. The dimeric diketopiperazine (DKPs) alkaloids are a diverse family of natural products (NPs) whose unique structural architectures and biological activities have inspired the development of new synthetic methodologies to access these molecules. However, catalyst-controlled methods that enable the selective formation of constitutional and stereoisomeric dimers from a single monomer are lacking. To resolve this long-standing synthetic challenge, we sought to characterize the biosynthetic enzymes that assemble these NPs for application in biocatalytic syntheses. Genome mining enabled identification of the cytochrome P450, NzeB (Streptomyces sp. NRRL F-5053), which catalyzes both intermolecular carbon-carbon (C-C) and carbon-nitrogen (C-N) bond formation. To identify the molecular basis for the flexible site-selectivity, stereoselectivity, and chemoselectivity of NzeB, we obtained high-resolution crystal structures (1.5 Å) of the protein in complex with native and non-native substrates. This, to our knowledge, represents the first crystal structure of an oxidase catalyzing direct, intermolecular C-H amination. Site-directed mutagenesis was utilized to assess the role individual active-site residues play in guiding selective DKP dimerization. Finally, computational approaches were employed to evaluate plausible mechanisms regarding NzeB function and its ability to catalyze both C-C and C-N bond formation. These results provide a structural and computational rationale for the catalytic versatility of NzeB, as well as new insights into variables that control selectivity of CYP450 diketopiperazine dimerases.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
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DOI of Published Version
https://doi.org/10.1021/JACS.0C06312
