› 4pbr

X-ray diffraction
1.9Å resolution

Crystal structure of the M. jannaschii G2 tRNA synthetase variant bound to 4-(2-bromoisobutyramido)-phenylalanine (BibaF)

Released:
DOI: 10.2210/pdb4pbr/pdb
PDB entry 4pbr coloured by chain, front view.
PDB entry 4pbr coloured by chain, side view.
PDB entry 4pbr coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii DSM 2661
Primary publication:
Gleaning unexpected fruits from hard-won synthetases: probing principles of permissivity in non-canonical amino acid-tRNA synthetases.
Cooley RB, Karplus PA, Mehl RA
Chembiochem 15 1810-9 (2014)
PMID: 25044993

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: 36.11 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q57834 (Residues: 1-306; Coverage: 100%)
Gene names: MJ0389, tyrS
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 2L7 1 x 2L7
Ligand PEG 1 x PEG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P43212
Unit cell:
a: 101.26Å b: 101.26Å c: 71.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.194 0.243
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Inverse electron demand Diels-Alder reactions in chemical biology.
Oliveira et al. (2017)
5 more

5 mentions without citation

Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria.
Luo et al. (2017)
4 more