› 2dlc

X-ray diffraction
2.4Å resolution

Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase

Released:
DOI: 10.2210/pdb2dlc/pdb
PDB entry 2dlc coloured by chain, front view.
PDB entry 2dlc coloured by chain, side view.
PDB entry 2dlc coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.
Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT
Nucleic Acids Res 35 4289-300 (2007)
PMID: 17576676

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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153187 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Tyrosine--tRNA ligase, cytoplasmic Chain: X
Molecule details ›
Chain: X
Length: 394 amino acids
Theoretical weight: 44.08 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36421 (Residues: 1-394; Coverage: 100%)
Gene names: G7522, MGM104, TYS1, YGR185C
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:
T-RNA (76-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 76 nucleotides
Theoretical weight: 24.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand YMP 1 x YMP
9 modified residues:
Ligand 2MG 1 x 2MG
Ligand H2U 1 x H2U
Ligand OMG 1 x OMG
Ligand M2G 1 x M2G
Ligand PSU 3 x PSU
Ligand 6IA 1 x 6IA
Ligand 5MC 1 x 5MC
Ligand 5MU 1 x 5MU
Ligand 1MA 1 x 1MA

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P41212
Unit cell:
a: 63.854Å b: 63.854Å c: 330.334Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.245 0.289
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

The nonribosomal synthesis of diketopiperazines in tRNA-dependent cyclodipeptide synthase pathways.
Belin et al. (2012)
7 more

21 mentions without citation

Fast, comprehensive two-dimensional liquid chromatography.
Stoll et al. (2007)
20 more