› 2zod

X-ray diffraction
1.98Å resolution

Crystal structure of selenophosphate synthetase from Aquifex aeolicus

Released:
DOI: 10.2210/pdb2zod/pdb
PDB entry 2zod coloured by chain, front view.
PDB entry 2zod coloured by chain, side view.
PDB entry 2zod coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
Itoh Y, Sekine S, Matsumoto E, Akasaka R, Takemoto C, Shirouzu M, Yokoyama S
J Mol Biol 385 1456-69 (2009)
PMID: 18773910

Function and Biology Details

Reaction catalysed: 
ATP + selenide + H(2)O = AMP + selenophosphate + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130449 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Selenide, water dikinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 345 amino acids
Theoretical weight: 37.7 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O67139 (Residues: 1-336; Coverage: 100%)
Gene names: aq_1030, selD
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 47.277Å b: 76.871Å c: 84.26Å
α: 90° β: 101.1° γ: 90°
R-values:
R R work R free
0.204 0.204 0.24
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The unique tRNASec and its role in selenocysteine biosynthesis.
Serrão et al. (2018)
2 more

3 mentions without citation

Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins.
Yang et al. (2017)
2 more