› 1td2

X-ray diffraction
2.22Å resolution

Crystal Structure of the PdxY Protein from Escherichia coli

Released:
DOI: 10.2210/pdb1td2/pdb
PDB entry 1td2 coloured by chain, front view.
PDB entry 1td2 coloured by chain, side view.
PDB entry 1td2 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of the PdxY Protein from Escherichia coli.
Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V
J Bacteriol 186 8074-82 (2004)
PMID: 15547280

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
Molecule details ›
Chains: A, B
Length: 287 amino acids
Theoretical weight: 31.36 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P77150 (Residues: 1-287; 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 PXL 2 x PXL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P21
Unit cell:
a: 63.13Å b: 67.375Å c: 73.589Å
α: 90° β: 93.67° γ: 90°
R-values:
R R work R free
0.194 0.176 0.246
Expression system: Escherichia coli

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Citations

3 review citations

Vitamin B6: a long known compound of surprising complexity.
Mooney et al. (2009)
2 more

6 mentions without citation

DNA glycosylases search for and remove oxidized DNA bases.
Wallace SS. (2013)
5 more