› 2du5

X-ray diffraction
3.2Å resolution

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with tRNAOpal and O-phosphoserine ("opal complex")

Released:
DOI: 10.2210/pdb2du5/pdb
PDB entry 2du5 coloured by chain, front view.
PDB entry 2du5 coloured by chain, side view.
PDB entry 2du5 coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Primary publication:
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
Fukunaga R, Yokoyama S
Nat Struct Mol Biol 14 272-9 (2007)
PMID: 17351629

Function and Biology Details

Reaction catalysed: 
ATP + O-phospho-L-serine + tRNA(Cys) = AMP + diphosphate + O-phospho-L-seryl-tRNA(Cys)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128219 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
O-phosphoserine--tRNA(Cys) ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 534 amino acids
Theoretical weight: 61.24 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O30126 (Residues: 1-534; Coverage: 100%)
Gene names: AF_0110, sepS
Sequence domains:
Structure domains:
tRNA Chain: D
Molecule details ›
Chain: D
Length: 71 nucleotides
Theoretical weight: 22.89 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P3121
Unit cell:
a: 148.04Å b: 148.04Å c: 152.483Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.223 0.223 0.299
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

From one amino acid to another: tRNA-dependent amino acid biosynthesis.
Sheppard et al. (2008)
6 more

2 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
1 more