› 2ddw

X-ray diffraction
3.2Å resolution

Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution

Released:
DOI: 10.2210/pdb2ddw/pdb
PDB entry 2ddw coloured by chain, front view.
PDB entry 2ddw coloured by chain, side view.
PDB entry 2ddw coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V
J Bacteriol 188 4542-52 (2006)
PMID: 16740960

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154048 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxine/pyridoxal/pyridoxamine kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 283 amino acids
Theoretical weight: 30.88 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P40191 (Residues: 1-283; Coverage: 100%)
Gene names: JW2411, b2418, pdxK, yfeI
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

1 bound ligand:
Ligand PXL 2 x PXL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 65.668Å b: 75.028Å c: 109.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.237 0.254
Expression system: Escherichia coli

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Citations

5 review citations

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

2 mentions without citation

Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
Safo et al. (2006)
1 more