Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis
- Harvard University, United States
- Pennsylvania State University, United States
Abstract
The cyanobacterial enzyme CylK assembles the cylindrocyclophane natural products by performing two unusual alkylation reactions, forming new carbon-carbon bonds between aromatic rings and secondary alkyl halide substrates. This transformation is unprecedented in biology and the structure and mechanism of CylK are unknown. Here, we report x-ray crystal structures of CylK, revealing a distinctive fusion of a Ca2+ binding domain and a β-propeller fold. We use a mutagenic screening approach to locate CylK's active site at its domain interface, identifying two residues, Arg105 and Tyr473, that are required for catalysis. Anomalous diffraction datasets collected with bound bromide ions, a product analog, suggest these residues interact with the alkyl halide electrophile. Additional mutagenesis and molecular dynamics simulations implicates Asp440 in activating the nucleophilic aromatic ring. Bioinformatic analysis of CylK homologs from other cyanobacteria establishes that they conserve these key catalytic amino acids but they are likely associated with divergent reactivity and altered secondary metabolism. By gaining a molecular understanding of this unusual biosynthetic transformation, this work fills a gap in our understanding of how alkyl halides are activated and used by enzymes as biosynthetic intermediates, informing enzyme engineering, catalyst design, and natural product discovery.
Data availability
Diffraction data have been deposited in the PDB under the accession codes 7RON, 7ROO. All other data generated or analyzed during this study and included in the manuscript and supporting files; Source Data files have been provided for Figure 4.
Article and author information
Author details
Funding
National Science Foundation (1454007)
- Emily P Balskus
National Science Foundation (2003436)
- Emily P Balskus
Research Corporation for Science Advancement (Cottrell Scholar Award)
- Emily P Balskus
National Institutes of Health (GM119707)
- Amie K Boal
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Braffman et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis
eLife 11:e75761.
https://doi.org/10.7554/eLife.75761
Further reading
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- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
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