› 1bw9

X-ray diffraction
1.5Å resolution

PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND PHENYLPYRUVATE

Released:
DOI: 10.2210/pdb1bw9/pdb
PDB entry 1bw9 coloured by chain, front view.
PDB entry 1bw9 coloured by chain, side view.
PDB entry 1bw9 coloured by chain, top view.
Source organism: Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Primary publication:
Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism.
Vanhooke JL, Thoden JB, Brunhuber NM, Blanchard JS, Holden HM
Biochemistry 38 2326-39 (1999)
PMID: 10029526

Function and Biology Details

Reaction catalysed: 
L-phenylalanine + H(2)O + NAD(+) = phenylpyruvate + NH(3) + NADH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176823 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Phenylalanine dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 356 amino acids
Theoretical weight: 36.56 KDa
Source organism: Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q59771 (Residues: 1-356; Coverage: 100%)
Gene name: pdh
Sequence domains:
Structure domains:
Phenylalanine dehydrogenase Chain: B
Molecule details ›
Chain: B
Length: 356 amino acids
Theoretical weight: 36.62 KDa
Source organism: Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q59771 (Residues: 1-356; Coverage: 100%)
Gene name: pdh
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
6 bound ligands:
Ligand PPY 2 x PPY
Ligand K 2 x K
Ligand NA 2 x NA
Ligand PO4 1 x PO4
Ligand EDO 3 x EDO
Ligand IPA 4 x IPA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 64.3Å b: 110.2Å c: 113.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 not available
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Role of Na+ and K+ in enzyme function.
Page et al. (2006)
2 more

4 mentions without citation

NAD(P)H-Dependent Dehydrogenases for the Asymmetric Reductive Amination of Ketones: Structure, Mechanism, Evolution and Application.
Sharma et al. (2017)
3 more