BER Structural Biology and Imaging Resources
Synchrotron, Neutron, and Cryo-EM
U.S. Department of Energy | Office of Science | Office of Biological and Environmental Research

Revealing a Peanut Family Secret for Making Chemical Building Blocks

June 26, 2017

Feature Story

The three-dimensional structure of the prephenate dehydrogenase (PDH) enzyme from the soybean legume. This structure helped show that only one mutation in PDH allowed legumes to evolve a new way to make the amino acid tyrosine. [Courtesy Cynthia Holland, Washington University in St. Louis]

Peanuts have a secret. It is a subtle one, but the peanut and its legume kin have not one, but two ways to make the tyrosine amino acid—one of 20 required to make all of this family’s proteins—an essential plant and human nutrient. Though a seemingly small feat, this unique way of making such an important chemical building block has been a mystery since its discovery in the 1960s. New research abetted by high-brightness X-ray beams is revealing how this second tyrosine pathway emerged in the legume family. Plant chemistry has evolved to make many different chemical compounds, many of which are important to human society, such as food, fiber, feed, fuel, and medicine. Starting from simpler compounds like tyrosine, these important molecules are precursors of countless interesting and useful chemicals such as morphine. The recently determined structure of the new plant enzyme could be a useful tool for biotechnologists trying to control the production of tyrosine and its derivatives. The team has tied this major evolutionary change in plant metabolism to a single mutation in the new enzyme.

In the 1960s and 1970s, scientists observed that plants used one pathway, known as arogenate dehydrogenase (ADH), to make tyrosine. They found that the legume family (i.e., peas, beans, and peanuts), however, had uniquely added a second, called prephenate dehydrogenase (PDH), previously known to be only in microbes. Two years ago, part of this team discovered the genes responsible for making tyrosine, learning that before peanuts and peas evolved into separate lineages, the legumes had evolved PDH enzymes from their existing ADH ones. These sister enzymes are very similar, so only a small number of changes could account for how ADH enzymes evolved into PDH ones. But there were still too many changes to test. The international collaborating teams purified the PDH enzyme of the soybean legume and determined its three-dimensional (3D) structure, which revealed that only a couple of mutations had occurred at the site where the chemical reactions take place. Instead of dozens of possible mutations, there were only two. Thus, changing a single amino acid in the center of the enzyme largely converted the soybean PDH enzyme back into its ancestor ADH enzyme, and this crucial switch also worked in reverse and for enzymes from multiple species. The scientists believe the legume PDH insensitivity to tyrosine could help to produce more tyrosine, and its useful derivatives, in systems like yeast or engineered plants.

Schenck, C. A., et al. “Molecular Basis of the Evolution of Alternative Tyrosine Biosynthetic Routes in Plants,” Nat. Chem. Biol. 13, 1029–1035 (2017). [DOI:10.1038/nchembio.2414].

Instruments and Facilities Used: Structural Biology Center (SBC)–CAT beam 19-ID of the Advanced Photon Source at Argonne National Laboratory.

Funding Acknowledgements: Work supported by the National Science Foundation (NSF; IOS-1354971 to H.A.M. and MCB-1614539 to J.M.J.). C.K.H. support: NSF Graduate Research Fellowship Program (DGE-1143954). Portions of research carried out at Argonne National Laboratory (ANL) Structural Biology Center (SBC) of the Advanced Photon Source (APS), a national user facility operated by the University of Chicago for the Office of Biological and Environmental Research (OBER), U.S. Department of Energy (DOE) Office of Science (DE-AC02-06CH11357).