› 4da0

X-ray diffraction
2.95Å resolution

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2'-deoxyguanosine

Released:
DOI: 10.2210/pdb4da0/pdb
PDB entry 4da0 coloured by chain, front view.
PDB entry 4da0 coloured by chain, side view.
PDB entry 4da0 coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.
de Giuseppe PO, Martins NH, Meza AN, dos Santos CR, Pereira HD, Murakami MT
PLoS One 7 e44282 (2012)
PMID: 22957058

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-128624 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chain: A
Molecule details ›
Chain: A
Length: 253 amino acids
Theoretical weight: 27.56 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O34925 (Residues: 1-233; Coverage: 100%)
Gene names: BSU19630, deoD, punB
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand GNG 1 x GNG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE W01B-MX2
Spacegroup: P6322
Unit cell:
a: 135.352Å b: 135.352Å c: 56.801Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.231 0.227 0.31
Expression system: Escherichia coli

Quick links

Citations

1 review citation

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

2 mentions without citation

Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.
de Giuseppe et al. (2012)
1 more