› 4ch5

X-ray diffraction
2.2Å resolution

Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl lysine

Released:
DOI: 10.2210/pdb4ch5/pdb
PDB entry 4ch5 coloured by chain, front view.
PDB entry 4ch5 coloured by chain, side view.
PDB entry 4ch5 coloured by chain, top view.
Source organism: Methanosarcina mazei Go1
Primary publication:
Structural basis for the site-specific incorporation of lysine derivatives into proteins.
Flügel V, Vrabel M, Schneider S
PLoS One 9 e96198 (2014)
PMID: 24760130

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: 33.42 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Escherichia coli BL21(DE3)
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

4 bound ligands:
Ligand YLP 1 x YLP
Ligand MG 1 x MG
Ligand EDO 5 x EDO
Ligand POP 1 x POP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P64
Unit cell:
a: 105.376Å b: 105.376Å c: 70.801Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.174 0.189
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Playing with the Molecules of Life.
Young et al. (2018)
2 more

1 mention without citation

Structural basis for the site-specific incorporation of lysine derivatives into proteins.
Flügel et al. (2014)