› 5ugf

X-ray diffraction
2.2Å resolution

Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate

Released:
DOI: 10.2210/pdb5ugf/pdb
PDB entry 5ugf coloured by chain, front view.
PDB entry 5ugf coloured by chain, side view.
PDB entry 5ugf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase.
Harijan RK, Zoi I, Antoniou D, Schwartz SD, Schramm VL
Proc Natl Acad Sci U S A 114 6456-6461 (2017)
PMID: 28584087

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132560 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 320 amino acids
Theoretical weight: 35.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P00491 (Residues: 1-289; Coverage: 100%)
Gene names: NP, PNP
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand PO4 29 x PO4
Ligand IM5 6 x IM5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 104.96Å b: 124.27Å c: 136.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.214 0.238
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

3 review citations

Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence.
Schramm et al. (2018)
2 more

1 mention without citation

Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase.
Harijan et al. (2017)