› 4r2w

X-ray diffraction
1.6Å resolution

X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution

Released:
DOI: 10.2210/pdb4r2w/pdb
PDB entry 4r2w coloured by chain, front view.
PDB entry 4r2w coloured by chain, side view.
PDB entry 4r2w coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.
Safonova TN, Mikhailov SN, Veiko VP, Mordkovich NN, Manuvera VA, Alekseev CS, Kovalchuk MV, Popov VO, Polyakov KM
Acta Crystallogr D Biol Crystallogr 70 3310-9 (2014)
PMID: 25478848

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184329 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 252 amino acids
Theoretical weight: 26.88 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8E9X9 (Residues: 1-252; Coverage: 100%)
Gene names: SO_4133, udp
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand SO4 8 x SO4
Ligand GOL 6 x GOL
Ligand URI 1 x URI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7A
Spacegroup: P21
Unit cell:
a: 91.92Å b: 96.48Å c: 91.93Å
α: 90° β: 120.01° γ: 90°
R-values:
R R work R free
0.178 0.177 0.192
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis.
Youn et al. (2016)
1 more

1 mention without citation

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