› 8dqh

X-ray diffraction
1.52Å resolution

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (RS1) bound to ATP and acridone after 24 hours of crystal growth

Released:
DOI: 10.2210/pdb8dqh/pdb
PDB entry 8dqh coloured by chain, front view.
PDB entry 8dqh coloured by chain, side view.
PDB entry 8dqh coloured by chain, top view.
Source organism: Candidatus Methanomethylophilus alvus
Primary publication:
Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity.
Gottfried-Lee I, Perona JJ, Karplus PA, Mehl RA, Cooley RB
ACS Chem Biol (2022)
PMID: 36395426

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104875 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminoacyl-transfer RNA synthetases class-II family profile domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 276 amino acids
Theoretical weight: 30.69 KDa
Source organism: Candidatus Methanomethylophilus alvus
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A3G3IHP7 (Residues: 2-275; Coverage: 100%)
Gene name: BKD89_05515
Sequence domains: Phenylalanyl tRNA synthetase beta chain CLM domain

Ligands and Environments

5 bound ligands:
Ligand ATP 2 x ATP
Ligand T7Q 1 x T7Q
Ligand PEG 1 x PEG
Ligand MG 5 x MG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: I4
Unit cell:
a: 110.862Å b: 110.862Å c: 113.556Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.177
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

Generating Efficient Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetases for Structurally Diverse Non-Canonical Amino Acids.
Avila-Crump et al. (2022)
4 more

1 mention without citation

Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity.
Gottfried-Lee et al. (2022)