› 1zm7

X-ray diffraction
2.2Å resolution

Crystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in complex with dTTP

Released:
DOI: 10.2210/pdb1zm7/pdb
PDB entry 1zm7 coloured by chain, front view.
PDB entry 1zm7 coloured by chain, side view.
PDB entry 1zm7 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D.
Welin M, Skovgaard T, Knecht W, Zhu C, Berenstein D, Munch-Petersen B, Piskur J, Eklund H
FEBS J 272 3733-42 (2005)
PMID: 16008571

Function and Biology Details

Reaction catalysed: 
ATP + a 2'-deoxyribonucleoside = ADP + a 2'-deoxyribonucleoside 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195062 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxynucleoside kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 230 amino acids
Theoretical weight: 26.91 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9XZT6 (Residues: 1-230; Coverage: 92%)
Gene names: CG5452, dnk
Sequence domains: Deoxynucleoside kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand TTP 4 x TTP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21
Unit cell:
a: 67.04Å b: 119.27Å c: 68.388Å
α: 90° β: 92.59° γ: 90°
R-values:
R R work R free
0.213 0.212 0.237
Expression system: Escherichia coli BL21

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Citations

1 review citation

Enzymes to die for: exploiting nucleotide metabolizing enzymes for cancer gene therapy.
Ardiani et al. (2012)
7 other articles