› 6yjz

X-ray diffraction
2.45Å resolution

Crystal structure of mouse pyridoxal kinase in apo form

Released:
DOI: 10.2210/pdb6yjz/pdb
PDB entry 6yjz coloured by chain, front view.
PDB entry 6yjz coloured by chain, side view.
PDB entry 6yjz coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission.
Kasaragod VB, Pacios-Michelena A, Schaefer N, Zheng F, Bader N, Alzheimer C, Villmann C, Schindelin H
Proc Natl Acad Sci U S A 117 33235-33245 (2020)
PMID: 33318193

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-185047 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 314 amino acids
Theoretical weight: 35.21 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8K183 (Residues: 1-312; Coverage: 100%)
Gene names: Pdxk, Pkh
Sequence domains: Phosphomethylpyrimidine kinase

Ligands and Environments

3 bound ligands:
Ligand PG4 2 x PG4
Ligand GOL 5 x GOL
Ligand EDO 15 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 279.135Å b: 53.433Å c: 109.372Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.26
Expression system: Escherichia coli

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Citations

3 review citations

Vitamin B-6-Induced Neuropathy: Exploring the Mechanisms of Pyridoxine Toxicity.
Hadtstein et al. (2021)
2 more