› 3kvy

X-ray diffraction
2.3Å resolution

Trapping of an oxocarbenium ion intermediate in UP crystals

Released:
DOI: 10.2210/pdb3kvy/pdb
PDB entry 3kvy coloured by chain, front view.
PDB entry 3kvy coloured by chain, side view.
PDB entry 3kvy coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Glycal formation in crystals of uridine phosphorylase.
Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE
Biochemistry 49 3499-509 (2010)
PMID: 20364833

Function and Biology Details

Reaction catalysed: 
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107715 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 309 amino acids
Theoretical weight: 33.92 KDa
Source organism: Bos taurus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5PJH9 (Residues: 1-309; Coverage: 100%)
Gene name: UPP1
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand SO4 4 x SO4
Ligand URA 2 x URA
Ligand R2B 2 x R2B
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P41212
Unit cell:
a: 83.478Å b: 83.478Å c: 260.063Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 citation in other articles

The products of 5-fluorouridine by the action of the pseudouridine synthase TruB disfavor one mechanism and suggest another.
Miracco et al. (2011)
10 more

1 mention without citation

Glycal formation in crystals of uridine phosphorylase.
Paul et al. (2010)