› 3adb

X-ray diffraction
2.8Å resolution

Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 1)

Released:
DOI: 10.2210/pdb3adb/pdb
PDB entry 3adb coloured by chain, front view.
PDB entry 3adb coloured by chain, side view.
PDB entry 3adb coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.
Chiba S, Itoh Y, Sekine S, Yokoyama S
Mol Cell 39 410-20 (2010)
PMID: 20705242

Function and Biology Details

Reaction catalysed: 
ATP + L-seryl-tRNA(Sec) = ADP + O-phospho-L-seryl-tRNA(Sec)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176714 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
L-seryl-tRNA(Sec) kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 259 amino acids
Theoretical weight: 31.2 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58933 (Residues: 1-248; Coverage: 100%)
Gene names: MJ1538, pstK
Sequence domains: Chromatin associated protein KTI12
Structure domains:
selenocysteine tRNA Chains: C, D
Molecule details ›
Chains: C, D
Length: 92 nucleotides
Theoretical weight: 29.71 KDa
Source organism: Methanopyrus kandleri
Expression system: Not provided
Sequence domains: Selenocysteine transfer RNA

Ligands and Environments

3 bound ligands:
Ligand PO4 1 x PO4
Ligand ANP 1 x ANP
Ligand MG 1 x MG
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU, PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21212
Unit cell:
a: 92.196Å b: 260.923Å c: 45.558Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.228 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Selenoproteins: molecular pathways and physiological roles.
Labunskyy et al. (2014)
5 more

12 mentions without citation

Automated 3D structure composition for large RNAs.
Popenda et al. (2012)
11 more