› 6k5h

X-ray diffraction
2.5Å resolution

Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.

Released:
DOI: 10.2210/pdb6k5h/pdb
PDB entry 6k5h coloured by chain, front view.
PDB entry 6k5h coloured by chain, side view.
PDB entry 6k5h coloured by chain, top view.
Source organism: Phytophthora capsici LT1534
Primary publication:
Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici.
Yang C, Li J, Huang Z, Zhang X, Gao X, Zhu C, Morris PF, Zhang X
Sci Rep 10 9051 (2020)
PMID: 32493959

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-105014 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside phosphorylase domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 309 amino acids
Theoretical weight: 33.15 KDa
Source organism: Phytophthora capsici LT1534
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A410UCT3 (Residues: 1-296; Coverage: 100%)
Gene name: up
Sequence domains: Phosphorylase superfamily

Ligands and Environments

2 bound ligands:
Ligand URA 4 x URA
Ligand R1P 4 x R1P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Unit cell:
a: 66.975Å b: 97.688Å c: 188.865Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.261 0.256 0.349
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type.
Mohammad et al. (2021)
2 more

1 mention without citation

Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici.
Yang et al. (2020)