Structural Biology of Aromatic Amino Acid Biosynthesis in Plants: The Prephenate Branch Point

Abstract

Plants are chemists that have spent the last 425 million years evolving unique secondary metabolites to communicate with their surroundings, defend themselves against pathogens, insects, and herbivores, and grow and develop. Many secondary metabolites are biosynthesized from the aromatic amino acids tryptophan, tyrosine, and phenylalanine, and the shikimate and aromatic amino acid biosynthetic pathways link primary and specialized metabolism. Prephenate aminotransferase (PAT) is a key enzyme in aromatic amino acid biosynthesis because its product, arogenate, is the immediate precursor for both tyrosine and phenylalanine. Interestingly, the enzyme has a dual role in metabolism and can also function as a classical aspartate aminotransferase. AtPAT is pyridoxal 5′‐phosphate‐dependent (PLP) enzyme belonging to the AAT‐like aspartate aminotransferase domain and follows a ping‐pong bi‐bi reaction mechanism through Schiff‐base formation to a catalytic K306 in the active site. Each subunit of the AtPAT dimer consists of a large domain and a small domain that belong to the α‐β class of protein fold. Despite the structural similarities to aspartate aminotransferases, the molecular basis of prephenate binding specificity remains elusive. To gain an understanding of the enzyme's chemistry and substrate selectivity, a 2.5 Å x‐ray structure of PAT from the model plant Arabidopsis thaliana (thale cress) was solved in complex with the PLP. To our knowledge, this is the first structure of a bona fide prephenate aminotransferase. Amino acid sequence comparisons of all known functional PATs shows that T84 and K169 are highly conserved; however, some enzymes annotated as PAT display sequence variations at these positions. Biochemical analysis of T84V, K169V, and T84V/K169V PAT reveals that the double mutant gained tyrosine aminotransferase activity and was able to convert 4‐hydroxyphenylpyruvate to tyrosine. T84 is on the opposite side of the active site pocket, while the amine backbone of K169 hydrogen bonds to PLP. We hypothesize that Thr84 and Lys169 are important for substrate recognition in the active site and will use these mutants in future crystallographic experiments. Overall, our structural studies will assist in understanding the role of this bi‐functional enzyme in the context of aromatic amino acid biosynthesis in plants.Support or Funding InformationThis material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE‐1143954. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Results shown in this report are derived from work performed at Argonne National Laboratory, Structural Biology Center at the Advanced Photon Source. Argonne is operated by UChicago Argonne, LLC, for the U.S. Department of Energy, Office of Biological and Environmental Research under contract DE‐AC02‐06CH11357.