Download MendeleyStructure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase.
Shende, V.V., Khatri, Y., Newmister, S.A., Sanders, J.N., Lindovska, P., Yu, F., Doyon, T.J., Kim, J., Houk, K.N., Movassaghi, M., Sherman, D.H.(2020) J Am Chem Soc 142: 17413-17424
- PubMed: 32786740
- DOI: https://doi.org/10.1021/jacs.0c06312
- Primary Citation of Related Structures:
6XAI, 6XAJ, 6XAK, 6XAL, 6XAM - PubMed Abstract:
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.
Organizational Affiliation:
Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States.
