› 2zim

X-ray diffraction
2.1Å resolution

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate

Released:
DOI: 10.2210/pdb2zim/pdb
PDB entry 2zim coloured by chain, front view.
PDB entry 2zim coloured by chain, side view.
PDB entry 2zim coloured by chain, top view.
Source organism: Methanosarcina mazei
Primary publication:
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.
Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Söll D, Steitz TA
Proc Natl Acad Sci U S A 104 11268-73 (2007)
PMID: 17592110

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
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

3 bound ligands:
Ligand EDO 10 x EDO
Ligand YLY 1 x YLY
Ligand POP 1 x POP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OTHER
Spacegroup: P64
Unit cell:
a: 105.07Å b: 105.07Å c: 70.262Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.228
Expression system: Escherichia coli

Quick links

Citations

23 review citations

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

18 mentions without citation

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