› 6wrq

X-ray diffraction
1.85Å resolution

Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) S158C variant bound to 3-nitro-tyrosine

Released:
DOI: 10.2210/pdb6wrq/pdb
PDB entry 6wrq coloured by chain, front view.
PDB entry 6wrq coloured by chain, side view.
PDB entry 6wrq coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii DSM 2661
Primary publication:
Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase.
Beyer JN, Hosseinzadeh P, Gottfried-Lee I, Van Fossen EM, Zhu P, Bednar RM, Karplus PA, Mehl RA, Cooley RB
J Mol Biol 432 4690-4704 (2020)
PMID: 32569745

Function and Biology Details

Reaction catalysed: 
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176482 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 314 amino acids
Theoretical weight: 36.1 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57834 (Residues: 1-306; Coverage: 100%)
Gene names: MJ0389, tyrS
Sequence domains: tRNA synthetases class I (W and Y)

Ligands and Environments

3 bound ligands:
Ligand GOL 2 x GOL
Ligand NA 1 x NA
Ligand NIY 2 x NIY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P43212
Unit cell:
a: 102Å b: 102Å c: 71.66Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.182 0.206
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Protein Tyrosine Nitration in Plant Nitric Oxide Signaling.
León J. (2022)
2 more

1 mention without citation

Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase.
Beyer et al. (2020)