› 3byx

X-ray diffraction
2.4Å resolution

Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 in Multiple Binding Modes

Released:
DOI: 10.2210/pdb3byx/pdb
PDB entry 3byx coloured by chain, front view.
PDB entry 3byx coloured by chain, side view.
PDB entry 3byx coloured by chain, top view.
Source organism: Lacticaseibacillus casei
Primary publication:
Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening.
Mangani S, Cancian L, Leone R, Pozzi C, Lazzari S, Luciani R, Ferrari S, Costi MP
J Med Chem 54 5454-67 (2011)
PMID: 21696158

Function and Biology Details

Reaction catalysed: 
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132544 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate synthase Chain: A
Molecule details ›
Chain: A
Length: 316 amino acids
Theoretical weight: 36.63 KDa
Source organism: Lacticaseibacillus casei
Expression system: Escherichia coli
UniProt:
  • Canonical: P00469 (Residues: 1-316; Coverage: 100%)
Gene name: thyA
Sequence domains: Thymidylate synthase
Structure domains: Thymidylate synthase/dCMP hydroxymethylase domain

Ligands and Environments

2 bound ligands:
Ligand UMP 1 x UMP
Ligand C00 1 x C00
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P6122
Unit cell:
a: 77.012Å b: 77.012Å c: 213.97Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.208 0.204 0.283
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS).
Pozzi et al. (2019)
3 other articles

1 mention without citation

Antifolate agents: a patent review (2006 - 2010).
Wright et al. (2011)