5T95 image
Deposition Date 2016-09-09
Release Date 2017-06-28
Last Version Date 2023-10-04
Entry Detail
PDB ID:
5T95
Keywords:
Title:
Prephenate Dehydrogenase M219T, N222D mutant from Soybean
Biological Source:
Source Organism:
Glycine max (Taxon ID: 3847)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.69 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Prephenate dehydrogenase 1
Gene (Uniprot):PDH1
Mutations:M219T, N222D
Chain IDs:A, B
Chain Length:271
Number of Molecules:2
Biological Source:Glycine max
Primary Citation
Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.
Nat. Chem. Biol. 13 1029 1035 (2017)
PMID: 28671678 DOI: 10.1038/nchembio.2414

Abstact

L-Tyrosine (Tyr) is essential for protein synthesis and is a precursor of numerous specialized metabolites crucial for plant and human health. Tyr can be synthesized via two alternative routes by different key regulatory TyrA family enzymes, prephenate dehydrogenase (PDH, also known as TyrAp) or arogenate dehydrogenase (ADH, also known as TyrAa), representing a unique divergence of primary metabolic pathways. The molecular foundation underlying the evolution of these alternative Tyr pathways is currently unknown. Here we characterized recently diverged plant PDH and ADH enzymes, obtained the X-ray crystal structure of soybean PDH, and identified a single amino acid residue that defines TyrA substrate specificity and regulation. Structures of mutated PDHs co-crystallized with Tyr indicate that substitutions of Asn222 confer ADH activity and Tyr sensitivity. Reciprocal mutagenesis of the corresponding residue in divergent plant ADHs further introduced PDH activity and relaxed Tyr sensitivity, highlighting the critical role of this residue in TyrA substrate specificity that underlies the evolution of alternative Tyr biosynthetic pathways in plants.

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Primary Citation of related structures