› 4c5l

X-ray diffraction
1.85Å resolution

Structure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal

Released:
DOI: 10.2210/pdb4c5l/pdb
PDB entry 4c5l coloured by chain, front view.
PDB entry 4c5l coloured by chain, side view.
PDB entry 4c5l coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus Mu50
Primary publication:
A subfamily of bacterial ribokinases utilizes a hemithioacetal for pyridoxal phosphate salvage.
Nodwell MB, Koch MF, Alte F, Schneider S, Sieber SA
J Am Chem Soc 136 4992-9 (2014)
PMID: 24601602

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-101970 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
pyridoxal kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 276 amino acids
Theoretical weight: 29.81 KDa
Source organism: Staphylococcus aureus subsp. aureus Mu50
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H3JTP0 (Residues: 2-276; Coverage: 100%)
Gene name: SAV0580
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand UEG 3 x UEG
Ligand SO4 4 x SO4
Ligand PXL 1 x PXL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 63.44Å b: 102.78Å c: 83.52Å
α: 90° β: 90.44° γ: 90°
R-values:
R R work R free
0.236 0.234 0.275
Expression system: Escherichia coli

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Citations

6 citation in other articles

Cellulase from Trichoderma harzianum interacts with roots and triggers induced systemic resistance to foliar disease in maize.
Saravanakumar et al. (2016)
5 more

1 mention without citation

Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP-dependent vitamin kinase family members.
Gonzalez-Ordenes et al. (2021)