› 4e1v

X-ray diffraction
2.15Å resolution

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

Released:
DOI: 10.2210/pdb4e1v/pdb
PDB entry 4e1v coloured by chain, front view.
PDB entry 4e1v coloured by chain, side view.
PDB entry 4e1v coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Primary publication:
X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae.
Lashkov AA, Sotnichenko SE, Prokofiev II, Gabdulkhakov AG, Agapov II, Shtil AA, Betzel C, Mironov AS, Mikhailov AM
Acta Crystallogr D Biol Crystallogr 68 968-74 (2012)
PMID: 22868762

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-140986 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chains: A, B, C, D, E, F, G, H, I
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I
Length: 253 amino acids
Theoretical weight: 27.17 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A1F6 (Residues: 1-253; Coverage: 100%)
Gene names: STM3968, STMD1.21, udp
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

4 bound ligands:
Ligand URF 8 x URF
Ligand GOL 5 x GOL
Ligand K 3 x K
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: C2
Unit cell:
a: 158.49Å b: 93.21Å c: 149.97Å
α: 90° β: 90.82° γ: 90°
R-values:
R R work R free
0.196 0.194 0.238
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Expression, purification, crystallization and preliminary X-ray structure analysis of Vibrio cholerae uridine phosphorylase in complex with thymidine.
Lashkov et al. (2012)

2 mentions without citation

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