› 5ud5

X-ray diffraction
2.35Å resolution

Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)

Released:
DOI: 10.2210/pdb5ud5/pdb
PDB entry 5ud5 coloured by chain, front view.
PDB entry 5ud5 coloured by chain, side view.
PDB entry 5ud5 coloured by chain, top view.
Source organism: Methanosarcina mazei Go1
Primary publication:
Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.
Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Söll D
Nat Chem Biol 13 1261-1266 (2017)
PMID: 29035363

Function and Biology Details

Reaction catalysed: 
ATP + L-pyrrolysine + tRNA(Pyl) = AMP + diphosphate + L-pyrrolysyl-tRNA(Pyl)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185816 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Pyrrolysine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 109 amino acids
Theoretical weight: 12.6 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8PWY1 (Residues: 1-101; Coverage: 22%)
Gene names: MM_1445, pylS
RNA (70-MER) Chains: C, D
Molecule details ›
Chains: C, D
Length: 72 nucleotides
Theoretical weight: 23.11 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3121
Unit cell:
a: 72.28Å b: 72.28Å c: 238.97Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.219 0.216 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

14 review citations

Reprogramming the genetic code.
de la Torre et al. (2021)
13 more

7 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
6 more