› 2cja

X-ray diffraction
2.2Å resolution

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP

Released:
DOI: 10.2210/pdb2cja/pdb
PDB entry 2cja coloured by chain, front view.
PDB entry 2cja coloured by chain, side view.
PDB entry 2cja coloured by chain, top view.
Source organism: Methanosarcina barkeri str. Fusaro
Primary publication:
Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition.
Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Söll D, Weygand-Durasevic I, Ban N
EMBO J 25 2498-509 (2006)
PMID: 16675947

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175172 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type-2 serine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 522 amino acids
Theoretical weight: 60.78 KDa
Source organism: Methanosarcina barkeri str. Fusaro
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q46AN5 (Residues: 1-502; Coverage: 100%)
Gene names: Mbar_A2126, serS2
Sequence domains: tRNA-binding domain
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand CL 2 x CL
Ligand ATP 2 x ATP
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 30 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3221
Unit cell:
a: 97.314Å b: 97.314Å c: 270.051Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.203 0.233
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology.
Ling et al. (2015)
2 more

4 mentions without citation

Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition.
Bilokapic et al. (2006)
3 more