› 2cim

X-ray diffraction
2.51Å resolution

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase

Released:
DOI: 10.2210/pdb2cim/pdb
PDB entry 2cim coloured by chain, front view.
PDB entry 2cim coloured by chain, side view.
PDB entry 2cim 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-559496 (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: 60.08 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

3 bound ligands:
Ligand ZN 2 x ZN
Ligand CL 2 x CL
Ligand PT 1 x PT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3221
Unit cell:
a: 97.15Å b: 97.15Å c: 268.5Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.202 0.199 0.252
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Aminoacyl-tRNA synthetases.
Rubio Gomez et al. (2020)
3 more

2 mentions without citation

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