› 1pk9

X-ray diffraction
1.9Å resolution

Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 2-fluoroadenosine and sulfate/phosphate

Released:
DOI: 10.2210/pdb1pk9/pdb
PDB entry 1pk9 coloured by chain, front view.
PDB entry 1pk9 coloured by chain, side view.
PDB entry 1pk9 coloured by chain, top view.
Source organism: Escherichia coli O157:H7
Primary publication:
Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase.
Bennett EM, Li C, Allan PW, Parker WB, Ealick SE
J Biol Chem 278 47110-8 (2003)
PMID: 12937174

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 domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142187 (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 O157:H7
UniProt:
  • Canonical: P0ABP9 (Residues: 2-238; Coverage: 99%)
Gene names: ECs5343, Z5986, deoD
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand PO4 3 x PO4
Ligand 2FA 3 x 2FA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P6122
Unit cell:
a: 122Å b: 122Å c: 241.9Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.192 0.265

Quick links

Citations

6 review citations

Purine-Metabolising Enzymes and Apoptosis in Cancer.
Camici et al. (2019)
5 more

4 mentions without citation

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