› 3zxi

X-ray diffraction
2.75Å resolution

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

Released:
DOI: 10.2210/pdb3zxi/pdb
PDB entry 3zxi coloured by chain, front view.
PDB entry 3zxi coloured by chain, side view.
PDB entry 3zxi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination
Bonnefond L, Schellenberger P, Basquin J, Demangeat G, Ritzenthaler C, Chenevert R, Balg C, Frugier M, Rudinger-Thirion J, Giege R, Lorber B, Sauter C
Cryst Growth Des 11 4334- (2011)

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 TYA 2 x TYA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 53.14Å b: 62.87Å c: 196.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.224 0.307
Expression system: Escherichia coli

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