› 3onv

X-ray diffraction
1.89Å resolution

Crystal structure of E. Coli purine nucleoside phosphorylase with SO4

Released:
DOI: 10.2210/pdb3onv/pdb
PDB entry 3onv coloured by chain, front view.
PDB entry 3onv coloured by chain, side view.
PDB entry 3onv coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Validation of the catalytic mechanism of Escherichia coli purine nucleoside phosphorylase by structural and kinetic studies.
Mikleušević G, Stefanić Z, Narczyk M, Wielgus-Kutrowska B, Bzowska A, Luić M
Biochimie 93 1610-22 (2011)
PMID: 21672603

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-142186 (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
Expression system: Escherichia coli
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

1 bound ligand:
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P6122
Unit cell:
a: 120.304Å b: 120.304Å c: 239.809Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.175 0.203
Expression system: Escherichia coli

Quick links

Citations

22 citation in other articles

Recombinant purine nucleoside phosphorylases from thermophiles: preparation, properties and activity towards purine and pyrimidine nucleosides.
Zhou et al. (2013)
21 more

1 mention without citation

Molecular replacement with a large number of molecules in the asymmetric unit.
Jobichen et al. (2014)