› 3ut6

X-ray diffraction
1.9Å resolution

Crystal structure of E. Coli PNP complexed with PO4 and formycin A

Released:
DOI: 10.2210/pdb3ut6/pdb
PDB entry 3ut6 coloured by chain, front view.
PDB entry 3ut6 coloured by chain, side view.
PDB entry 3ut6 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A.
Štefanić Z, Narczyk M, Mikleušević G, Wielgus-Kutrowska B, Bzowska A, Luić M
FEBS Lett 586 967-71 (2012)
PMID: 22569248

Function and Biology Details

Reaction catalysed: 
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-532705 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 237 amino acids
Theoretical weight: 25.72 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ABP8 (Residues: 2-238; Coverage: 99%)
Gene names: JW4347, b4384, deoD, pup
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand FMC 3 x FMC
Ligand PO4 5 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P6122
Unit cell:
a: 120.769Å b: 120.769Å c: 239.082Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.164 0.163 0.187

Quick links

Citations

5 citation in other articles

Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
Narczyk et al. (2018)
4 more

1 mention without citation

Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases.
Il'icheva et al. (2020)