› 1vi9

X-ray diffraction
1.96Å resolution

Function and Biology Details

Reaction catalysed: 
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160121 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal kinase PdxY Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 299 amino acids
Theoretical weight: 33.17 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P77150 (Residues: 2-287; Coverage: 100%)
Gene names: JW1628, b1636, pdxY, ydgS
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

2 bound ligands:
Ligand SO4 4 x SO4
Ligand BME 2 x BME
2 modified residues:
Ligand MSE 36 x MSE
Ligand CSD 4 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 32-ID
Spacegroup: P21
Unit cell:
a: 53.383Å b: 92.592Å c: 122.237Å
α: 90° β: 99.42° γ: 90°
R-values:
R R work R free
0.198 0.198 0.256
Expression system: Escherichia coli

Quick links

Citations

23 review citations

Regulation of fatty acid metabolism in bacteria.
Fujita et al. (2007)
22 more

1 mention without citation

Crystal structure of the PdxY Protein from Escherichia coli.
Safo et al. (2004)