› 2pid

X-ray diffraction
2.2Å resolution

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog

Released:
DOI: 10.2210/pdb2pid/pdb
PDB entry 2pid coloured by chain, front view.
PDB entry 2pid coloured by chain, side view.
PDB entry 2pid coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human mitochondrial tyrosyl-tRNA synthetase reveals common and idiosyncratic features.
Bonnefond L, Frugier M, Touzé E, Lorber B, Florentz C, Giegé R, Sauter C, Rudinger-Thirion J
Structure 15 1505-16 (2007)
PMID: 17997975

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195175 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosine--tRNA ligase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 356 amino acids
Theoretical weight: 39.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2Z4 (Residues: 32-375; Coverage: 72%)
Gene names: CGI-04, YARS2
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 54Å b: 62.4Å c: 194.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.193 0.244
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases.
Suzuki et al. (2011)
6 more

9 mentions without citation

When a common biological role does not imply common disease outcomes: Disparate pathology linked to human mitochondrial aminoacyl-tRNA synthetases.
González-Serrano et al. (2019)
8 more