› 2zin

X-ray diffraction
1.79Å resolution

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue

Released:
DOI: 10.2210/pdb2zin/pdb
PDB entry 2zin coloured by chain, front view.
PDB entry 2zin coloured by chain, side view.
PDB entry 2zin coloured by chain, top view.
Source organism: Methanosarcina mazei
Primary publication:
Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.
Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S
Chem Biol 15 1187-97 (2008)
PMID: 19022179

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 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.34 KDa
Source organism: Methanosarcina mazei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8PWY1 (Residues: 185-454; Coverage: 60%)
Gene names: MM_1445, pylS
Sequence domains: tRNA synthetases class II core domain (F)
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P64
Unit cell:
a: 104.71Å b: 104.71Å c: 70.55Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.19 0.222
Expression system: Escherichia coli

Quick links

Citations

30 review citations

Adding new chemistries to the genetic code.
Liu et al. (2010)
29 more

7 mentions without citation

Stereochemical basis for engineered pyrrolysyl-tRNA synthetase and the efficient in vivo incorporation of structurally divergent non-native amino acids.
Takimoto et al. (2011)
6 more