› 8ke6

X-ray diffraction
1.9Å resolution

PylRS C-terminus domain mutant bound with L-3-chlorophenylalanine and AMPNP

Released:
DOI: 10.2210/pdb8ke6/pdb
PDB entry 8ke6 coloured by chain, front view.
PDB entry 8ke6 coloured by chain, side view.
PDB entry 8ke6 coloured by chain, top view.
Source organism: Methanosarcina mazei
Primary publication:
Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids.
Jiang HK, Weng JH, Wang YH, Tsou JC, Chen PJ, Ko AA, Söll D, Tsai MD, Wang YS
OpenAccess logo Front Genet 14 1277489 (2023)
PMID: 37904728

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

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: 277 amino acids
Theoretical weight: 32 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)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P64
Unit cell:
a: 105.162Å b: 105.162Å c: 72.446Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.174 0.173 0.188
Expression system: Escherichia coli

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