› 6f52

X-ray diffraction
2Å resolution

Crystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and formycin A

Released:
DOI: 10.2210/pdb6f52/pdb
PDB entry 6f52 coloured by chain, front view.
PDB entry 6f52 coloured by chain, side view.
PDB entry 6f52 coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
Narczyk M, Bertoša B, Papa L, Vuković V, Leščić Ašler I, Wielgus-Kutrowska B, Bzowska A, Luić M, Štefanić Z
FEBS J 285 1305-1325 (2018)
PMID: 29430816

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-157474 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 233 amino acids
Theoretical weight: 25.82 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P56463 (Residues: 1-233; Coverage: 100%)
Gene names: HP_1178, deoD
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P21
Unit cell:
a: 83.617Å b: 64.792Å c: 140.727Å
α: 90° β: 99.37° γ: 90°
R-values:
R R work R free
0.207 0.205 0.246
Expression system: Escherichia coli BL21

Quick links

Citations

2 review citations

Helicobacter pylori treatment in the post-antibiotics era-searching for new drug targets.
Roszczenko-Jasińska et al. (2020)
1 more

1 mention without citation

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