› 4apz

X-ray diffraction
2.01Å resolution

Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1

Released:
DOI: 10.2210/pdb4apz/pdb
PDB entry 4apz coloured by chain, front view.
PDB entry 4apz coloured by chain, side view.
PDB entry 4apz coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Tying down the arm in Bacillus dUTPase: structure and mechanism.
García-Nafría J, Timm J, Harrison C, Turkenburg JP, Wilson KS
Acta Crystallogr D Biol Crystallogr 69 1367-80 (2013)
PMID: 23897460

Function and Biology Details

Reaction catalysed: 
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128374 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase YncF Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m
Molecule details ›
Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m
Length: 144 amino acids
Theoretical weight: 16.43 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O31801 (Residues: 1-144; Coverage: 100%)
Gene names: BSU17660, yncF
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

4 bound ligands:
Ligand DUR 48 x DUR
Ligand POP 48 x POP
Ligand MG 48 x MG
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P1
Unit cell:
a: 97.06Å b: 97.07Å c: 193.85Å
α: 89.72° β: 88.47° γ: 90.11°
R-values:
R R work R free
0.171 0.169 0.212
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.
Barabás et al. (2013)
4 more

1 mention without citation

Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes.
Li et al. (2019)