› 4yc4

X-ray diffraction
2.58Å resolution

Crystal structure of phosphatidyl inositol 4-kinase II alpha in complex with nucleotide analog

Released:
DOI: 10.2210/pdb4yc4/pdb
PDB entry 4yc4 coloured by chain, front view.
PDB entry 4yc4 coloured by chain, side view.
PDB entry 4yc4 coloured by chain, top view.
Source organisms:
Primary publication:
The high-resolution crystal structure of phosphatidylinositol 4-kinase IIβ and the crystal structure of phosphatidylinositol 4-kinase IIα containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design.
Klima M, Baumlova A, Chalupska D, Hřebabecký H, Dejmek M, Nencka R, Boura E
Acta Crystallogr D Biol Crystallogr 71 1555-63 (2015)
PMID: 26143926

Function and Biology Details

Reactions catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo-inositol 4-phosphate
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112951 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endolysin; Phosphatidylinositol 4-kinase type 2-alpha Chain: A
Molecule details ›
Chain: A
Length: 556 amino acids
Theoretical weight: 63.24 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BTU6 (Residues: 76-172, 180-468; Coverage: 81%)
  • Canonical: D9IEF7 (Residues: 2-164; Coverage: 99%)
Gene names: PI4K2A, T4Tp126, e
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand M59 1 x M59
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21212
Unit cell:
a: 79.414Å b: 103.77Å c: 78.109Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.256
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

A Plethora of Functions Condensed into Tiny Phospholipids: The Story of PI4P and PI(4,5)P2.
Bura et al. (2023)
1 more

2 mentions without citation

Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study.
Ware et al. (2021)
1 more