› 5k1x

X-ray diffraction
1.95Å resolution

Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant Y306A/N346A/C348A/Y384F in complex with AMPPNP

Released:
DOI: 10.2210/pdb5k1x/pdb
PDB entry 5k1x coloured by chain, front view.
PDB entry 5k1x coloured by chain, side view.
PDB entry 5k1x coloured by chain, top view.
Source organism: Methanosarcina mazei
Primary publication:
Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader.
Lee YJ, Schmidt MJ, Tharp JM, Weber A, Koenig AL, Zheng H, Gao J, Waters ML, Summerer D, Liu WR
Chem Commun (Camb) 52 12606-12609 (2016)
PMID: 27711380

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: 274 amino acids
Theoretical weight: 31.66 KDa
Source organism: Methanosarcina mazei
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8PWY1 (Residues: 188-454; Coverage: 59%)
Gene names: MM_1445, pylS
Sequence domains: tRNA synthetases class II core domain (F)
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ANP 1 x ANP
Ligand MG 2 x MG
Ligand EDO 1 x EDO
Ligand PEG 1 x PEG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 102.017Å b: 44.14Å c: 64.309Å
α: 90° β: 100.01° γ: 90°
R-values:
R R work R free
0.199 0.197 0.227
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Cation-π Interactions and their Functional Roles in Membrane Proteins.
Infield et al. (2021)
1 more