› 7em2

X-ray diffraction
2.6Å resolution

Crystal structure of the PI5P4Kbeta-XTP complex

Released:
DOI: 10.2210/pdb7em2/pdb
PDB entry 7em2 coloured by chain, front view.
PDB entry 7em2 coloured by chain, side view.
PDB entry 7em2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity.
Takeuchi K, Ikeda Y, Senda M, Harada A, Okuwaki K, Fukuzawa K, Nakagawa S, Yu HY, Nagase L, Imai M, Sasaki M, Lo YH, Ito D, Osaka N, Fujii Y, Sasaki AT, Senda T
Structure 30 886-899.e4 (2022)
PMID: 35504278

Function and Biology Details

Reaction catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol 5-phosphate = ADP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160254 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 393 amino acids
Theoretical weight: 44.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P78356 (Residues: 31-416; Coverage: 93%)
Gene names: PIP4K2B, PIP5K2B
Sequence domains: Phosphatidylinositol-4-phosphate 5-Kinase

Ligands and Environments

2 bound ligands:
Ligand CZC 2 x CZC
Ligand CZF 1 x CZF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: C2221
Unit cell:
a: 109.848Å b: 185.138Å c: 105.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.258
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ.
Takeuchi et al. (2023)
2 more

1 mention without citation

The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity.
Takeuchi et al. (2022)