› 4ttj

X-ray diffraction
1.87Å resolution

Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 6 FMC molecules

Released:
DOI: 10.2210/pdb4ttj/pdb
PDB entry 4ttj coloured by chain, front view.
PDB entry 4ttj coloured by chain, side view.
PDB entry 4ttj coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.
Štefanić Z, Narczyk M, Mikleušević G, Kazazić S, Bzowska A, Luić M
Sci Rep 8 15427 (2018)
PMID: 30337572

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, D
Molecule details ›
Chains: A, B, D
Length: 237 amino acids
Theoretical weight: 25.59 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
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

3 bound ligands:
Ligand PO4 3 x PO4
Ligand FMC 3 x FMC
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P6122
Unit cell:
a: 120.696Å b: 120.696Å c: 239.538Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.158 0.157 0.194
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit.
Medvedev et al. (2021)
3 more

2 mentions without citation

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