Beverly Fu

All Publications

• Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature's Known Radical Chemistry. Journal of the American Chemical Society Fu, B., Yang, H., Kountz, D. J., Lundahl, M. N., Beller, H. R., Broderick, W. E., Broderick, J. B., Hoffman, B. H., Balskus, E. P. 2024

  Abstract

  Radical enzymes, including the evolutionarily ancient glycyl radical enzyme (GRE) family, catalyze chemically challenging reactions that are involved in a myriad of important biological processes. All GREs possess an essential, conserved backbone glycine that forms a stable catalytically essential alpha-carbon radical. Through close examination of the GRE family, we unexpectedly identified hundreds of noncanonical GRE homologues that encode either an alanine, serine, or threonine in place of the catalytic glycine residue. Contrary to a long-standing belief, we experimentally demonstrate that these aminoacyl radical enzymes (AAREs) form stable alpha-carbon radicals on the three cognate residues when activated by partner activating enzymes. The previously unrecognized AAREs are widespread in microbial genomes, highlighting their biological importance and potential for exhibiting new reactivity. Collectively, these studies expand the known radical chemistry of living systems while raising questions about the evolutionary emergence of the AAREs.

  View details for DOI 10.1021/jacs.4c10348

  View details for PubMedID 39392720

• A cellular platform for production of C₄ monomers CHEMICAL SCIENCE Davis, M. A., Yu, V., Fu, B., Wen, M., Koleski, E. J., Silverman, J., Berdan, C. A., Nomura, D. K., Chang, M. C. Y. 2023

  View details for DOI 10.1039/d3sc02773b

  View details for Web of Science ID 001081057900001

• Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level CELL HOST & MICROBE Kenny, D. J., Plichta, D. R., Shungin, D., Koppel, N., Hall, A., Fu, B., Vasan, R. S., Shaw, S. Y., Vlamakis, H., Balskus, E. P., Xavier, R. J. 2020; 28 (2): 245-+

  Abstract

  The human microbiome encodes extensive metabolic capabilities, but our understanding of the mechanisms linking gut microbes to human metabolism remains limited. Here, we focus on the conversion of cholesterol to the poorly absorbed sterol coprostanol by the gut microbiota to develop a framework for the identification of functional enzymes and microbes. By integrating paired metagenomics and metabolomics data from existing cohorts with biochemical knowledge and experimentation, we predict and validate a group of microbial cholesterol dehydrogenases that contribute to coprostanol formation. These enzymes are encoded by ismA genes in a clade of uncultured microorganisms, which are prevalent in geographically diverse human cohorts. Individuals harboring coprostanol-forming microbes have significantly lower fecal cholesterol levels and lower serum total cholesterol with effects comparable to those attributed to variations in lipid homeostasis genes. Thus, cholesterol metabolism by these microbes may play important roles in reducing intestinal and serum cholesterol concentrations, directly impacting human health.

  View details for DOI 10.1016/j.chom.2020.05.013

  View details for Web of Science ID 000560392200013

  View details for PubMedID 32544460

  View details for PubMedCentralID PMC7435688

• Structural and Biochemical Studies of Substrate Selectivity in <i>Ascaris suum</i> Thiolases BIOCHEMISTRY Blaisse, M. R., Fu, B., Chang, M. C. Y. 2018; 57 (22): 3155-3166

  Abstract

  Thiolases are a class of carbon-carbon bond forming enzymes with important applications in biotechnology and metabolic engineering as they provide a general method for the condensation of two acyl coenzyme A (CoA) substrates. As such, developing a greater understanding of their substrate selectivity would expand our ability to engineer the enzymatic or microbial production of a broad range of small-molecule targets. Here, we report the crystal structures and biochemical characterization of Acat2 and Acat5, two biosynthetic thiolases from Ascaris suum with varying selectivity toward branched compared to linear compounds. The structure of the Acat2-C91S mutant bound to propionyl-CoA shows that the terminal methyl group of the substrate, representing the α-branch point, is directed toward the conserved Phe 288 and Met 158 residues. In Acat5, the Phe ring is rotated to accommodate a hydroxyl-π interaction with an adjacent Thr side chain, decreasing space in the binding pocket and possibly accounting for its strong preference for linear substrates compared to Acat2. Comparison of the different Acat thiolase structures shows that Met 158 is flexible, adopting alternate conformations with the side chain rotated toward or away from a covering loop at the back of the active site. Mutagenesis of residues in the covering loop in Acat5 with the corresponding residues from Acat2 allows for highly increased accommodation of branched substrates, whereas the converse mutations do not significantly affect Acat2 substrate selectivity. Our results suggest an important contribution of second-shell residues to thiolase substrate selectivity and offer insights into engineering this enzyme class.

  View details for DOI 10.1021/acs.biochem.7b01123

  View details for Web of Science ID 000434893900009

  View details for PubMedID 29381332