› 3vqx

X-ray diffraction
2.3Å resolution

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic crystal form

Released:
DOI: 10.2210/pdb3vqx/pdb
PDB entry 3vqx coloured by chain, front view.
PDB entry 3vqx coloured by chain, side view.
PDB entry 3vqx 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

Reaction catalysed: 
ATP + L-pyrrolysine + tRNA(Pyl) = AMP + diphosphate + L-pyrrolysyl-tRNA(Pyl)
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-185817 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolysine--tRNA ligase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 291 amino acids
Theoretical weight: 33.34 KDa
Source organism: Methanosarcina mazei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8PWY1 (Residues: 184-454; Coverage: 60%)
Gene names: MM_1445, pylS
Sequence domains: tRNA synthetases class II core domain (F)
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand AMP 2 x AMP
Ligand PO4 4 x PO4
Ligand BLK 2 x BLK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P1
Unit cell:
a: 62.798Å b: 69.422Å c: 83.326Å
α: 106.92° β: 91.41° γ: 113.83°
R-values:
R R work R free
0.212 0.212 0.27
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