› 2yye

X-ray diffraction
2.1Å resolution

Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP

Released:
DOI: 10.2210/pdb2yye/pdb
PDB entry 2yye coloured by chain, front view.
PDB entry 2yye coloured by chain, side view.
PDB entry 2yye coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
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 VF5
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O67139 (Residues: 1-336; Coverage: 100%)
Gene names: aq_1030, selD
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand CO 10 x CO
Ligand APC 2 x APC
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P3121
Unit cell:
a: 80.536Å b: 80.536Å c: 160.641Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.173 0.225
Expression system: Escherichia coli BL21

Quick links

Citations

3 review citations

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

2 mentions without citation

Structural biology of the purine biosynthetic pathway.
Zhang et al. (2008)
1 more