› 5h56

X-ray diffraction
1.7Å resolution

ADP and dTDP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5

Released:
DOI: 10.2210/pdb5h56/pdb
PDB entry 5h56 coloured by chain, front view.
PDB entry 5h56 coloured by chain, side view.
PDB entry 5h56 coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Primary publication:
Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate.
Biswas A, Shukla A, Chaudhary SK, Santhosh R, Jeyakanthan J, Sekar K
FEBS J 284 2527-2544 (2017)
PMID: 28627020

Function and Biology Details

Reaction catalysed: 
ATP + dTMP = ADP + dTDP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130444 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 195 amino acids
Theoretical weight: 22.4 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O67099 (Residues: 1-195; Coverage: 100%)
Gene names: aq_969, tmk
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

5 bound ligands:
Ligand ADP 2 x ADP
Ligand TYD 2 x TYD
Ligand MG 6 x MG
Ligand CA 2 x CA
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P21
Unit cell:
a: 42.482Å b: 62.414Å c: 76.144Å
α: 90° β: 91.02° γ: 90°
R-values:
R R work R free
0.157 0.156 0.185
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

The Binding Mechanism Between Inositol Phosphate (InsP) and the Jasmonate Receptor Complex: A Computational Study.
Cui et al. (2018)
4 more

1 mention without citation

Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate.
Biswas et al. (2017)