Aromatic amino acids are protein building blocks and precursors to a number of plant natural products, such as the structural polymer lignin and a variety of medicinally relevant compounds. Plants make tyrosine and phenylalanine by a different pathway from many microbes; this pathway requires prephenate aminotransferase (
Lignin is one of the most abundant biopolymers in nature and has great potential to be transformed into high-value chemicals. However, the limited availability of molecular structure data hinders its potential industrial applications. Herein, we present the Lignin Structural (LGS) Dataset that includes the molecular structure of milled wood lignin focusing on two major monomeric units (coniferyl and syringyl), and the six most common interunit linkages (phenylpropane β-aryl ether, resinol, phenylcoumaran, biphenyl, dibenzodioxocin, and diaryl ether). The dataset constitutes a unique resource that covers a part of lignin’s chemical space characterized by polymer chains with lengths in the range of 3 to 25 monomer units. Structural data were generated using a sequence-controlled polymer generation approach that was calibrated to match experimental lignin properties. The LGS dataset includes 60 K newly generated lignin structures that match with high accuracy (~90%) the experimentally determined structural compositions available in the literature. The LGS dataset is a valuable resource to advance lignin chemistry research, including computational simulation approaches and predictive modelling.
more » « less- NSF-PAR ID:
- 10376645
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Data
- Volume:
- 9
- Issue:
- 1
- ISSN:
- 2052-4463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Summary PAT ) as the key enzyme. Prephenate aminotransferase produces arogenate, the unique and immediate precursor for both tyrosine and phenylalanine in plants, and also has aspartate aminotransferase (AAT ) activity. The molecular mechanisms governing the substrate specificity and activation or inhibition ofPAT are currently unknown. Here we present the X‐ray crystal structures of the wild‐type and various mutants ofPAT fromArabidopsis thaliana (AtPAT ) . Steady‐state kinetic and ligand‐binding analyses identified key residues, such as Glu108, that are involved in both keto acid and amino acid substrate specificities and probably contributed to the evolution ofPAT activity among class IbAAT enzymes. Structures of AtPAT mutants co‐crystallized with either α‐ketoglutarate or pyridoxamine 5′‐phosphate and glutamate further define the molecular mechanisms underlying recognition of keto acid and amino acid substrates. Furthermore, cysteine was identified as an inhibitor ofPAT fromA. thaliana and Antirrhinum majus plants as well as the bacteriumChlorobium tepidum , uncovering a potential new effector ofPAT . -
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