› 3vqy

X-ray diffraction
2.4Å resolution

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)

Released:
DOI: 10.2210/pdb3vqy/pdb
PDB entry 3vqy coloured by chain, front view.
PDB entry 3vqy coloured by chain, side view.
PDB entry 3vqy coloured by chain, top view.
Source organism: Methanosarcina mazei
Primary publication:
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site.
Yanagisawa T, Sumida T, Ishii R, Yokoyama S
Acta Crystallogr D Biol Crystallogr 69 5-15 (2013)
PMID: 23275158

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164185 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolysine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.34 KDa
Source organism: Methanosarcina mazei
Expression system: Escherichia coli
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ANP 1 x ANP
Ligand LBY 1 x LBY
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P64
Unit cell:
a: 103.355Å b: 103.355Å c: 70.906Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.197 0.231
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool.
Wan et al. (2014)
2 more