› 2i5b

X-ray diffraction
2.8Å resolution

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution

Released:
DOI: 10.2210/pdb2i5b/pdb
PDB entry 2i5b coloured by chain, front view.
PDB entry 2i5b coloured by chain, side view.
PDB entry 2i5b coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.
Newman JA, Das SK, Sedelnikova SE, Rice DW
J Mol Biol 363 520-30 (2006)
PMID: 16978644

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-153905 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxine kinase Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 271 amino acids
Theoretical weight: 29.05 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P39610 (Residues: 1-271; Coverage: 100%)
Gene names: BSU38020, ipa-52r, pdxK, ywdB
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

1 bound ligand:
Ligand ADP 5 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P41212
Unit cell:
a: 102.499Å b: 102.499Å c: 251.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.222 0.274
Expression system: Escherichia coli BL21

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Citations

1 review citation

A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis.
Richts et al. (2019)
8 other articles

2 mentions without citation

Essential Metabolic Routes as a Way to ESKAPE From Antibiotic Resistance.
Barra et al. (2020)
1 more