› 2yaz

X-ray diffraction
2.4Å resolution

The Crystal Structure of Leishmania major dUTPase in complex dUMP

Released:
DOI: 10.2210/pdb2yaz/pdb
PDB entry 2yaz coloured by chain, front view.
PDB entry 2yaz coloured by chain, side view.
PDB entry 2yaz coloured by chain, top view.
Source organism: Leishmania major
Primary publication:
The crystal structure of the Leishmania major deoxyuridine triphosphate nucleotidohydrolase in complex with nucleotide analogues, dUMP, and deoxyuridine.
Hemsworth GR, Moroz OV, Fogg MJ, Scott B, Bosch-Navarrete C, González-Pacanowska D, Wilson KS
J Biol Chem 286 16470-81 (2011)
PMID: 21454646

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127546 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dUTPase Chains: A, B, D, E
Molecule details ›
Chains: A, B, D, E
Length: 271 amino acids
Theoretical weight: 30.61 KDa
Source organism: Leishmania major
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15826 (Residues: 1-268; Coverage: 100%)
Gene names: DUT, LMJF_06_0560, dut
Sequence domains: dUTPase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand UMP 4 x UMP
Ligand SO4 4 x SO4
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3121
Unit cell:
a: 109.11Å b: 109.11Å c: 309.311Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.203 0.225
Expression system: Escherichia coli BL21(DE3)

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Citations

5 review citations

Recent developments in drug discovery for leishmaniasis and human African trypanosomiasis.
Nagle et al. (2014)
4 more

2 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
1 more