6XAI

Crystal structure of NzeB in complex with cyclo-(L-Trp-L-Pro)

Summary for 6XAI

• Entry DOI: 10.2210/pdb6xai/pdb
• Descriptor: NzeB, PROTOPORPHYRIN IX CONTAINING FE, (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, ... (5 entities in total)
• Functional Keywords: monooxygenase, dimerase, p450, oxidoreductase
• Biological source: Streptomyces sp. NRRL F-5053
• Total number of polymer chains: 2
• Total formula weight: 90285.54

Authors

Shende, V.V.,Khatri, Y.,Newmister, S.A.,Sanders, J.N.,Lindovska, P.,Yu, F.,Doyon, T.J.,Kim, J.,Movassaghi, M.,Houk, K.N.,Sherman, D.H. (deposition date: 2020-06-04, release date: 2021-06-09, Last modification date: 2024-10-23)

Primary citation

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.
Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase.
J.Am.Chem.Soc., 142:17413-17424, 2020

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 ( 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.

PubMed: 32786740
DOI: 10.1021/jacs.0c06312

Experimental method

X-RAY DIFFRACTION (1.489 Å)