› 5t9f

X-ray diffraction
1.99Å resolution

Prephenate Dehydrogenase N222D mutant from Soybean

Released:
DOI: 10.2210/pdb5t9f/pdb
PDB entry 5t9f coloured by chain, front view.
PDB entry 5t9f coloured by chain, side view.
PDB entry 5t9f coloured by chain, top view.
Source organism: Glycine max
Primary publication:
Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.
Schenck CA, Holland CK, Schneider MR, Men Y, Lee SG, Jez JM, Maeda HA
Nat Chem Biol 13 1029-1035 (2017)
PMID: 28671678

Function and Biology Details

Reaction catalysed: 
Prephenate + NADP(+) = 4-hydroxyphenylpyruvate + CO(2) + NADPH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-515976 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prephenate/arogenate dehydrogenase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 271 amino acids
Theoretical weight: 30.68 KDa
Source organism: Glycine max
Expression system: Escherichia coli
UniProt:
  • Canonical: I1MYY4 (Residues: 1-271; Coverage: 100%)
Gene names: 100787362, GLYMA_18G023100, PDH1
Sequence domains: Prephenate dehydrogenase, nucleotide-binding domain

Ligands and Environments


Cofactor: Ligand NAP 2 x NAP
1 bound ligand:
Ligand TYR 2 x TYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P1
Unit cell:
a: 46.445Å b: 55.046Å c: 68.387Å
α: 107.82° β: 99.56° γ: 102.58°
R-values:
R R work R free
0.16 0.158 0.206
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity.
Maeda HA. (2019)
4 more

1 mention without citation

Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
Shabalin et al. (2020)