› 3vjr

X-ray diffraction
2.4Å resolution

Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the CCA-acceptor-T[PSI]C domain of tRNA

Released:
DOI: 10.2210/pdb3vjr/pdb
PDB entry 3vjr coloured by chain, front view.
PDB entry 3vjr coloured by chain, side view.
PDB entry 3vjr coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
Ito K, Murakami R, Mochizuki M, Qi H, Shimizu Y, Miura K, Ueda T, Uchiumi T
Nucleic Acids Res 40 10521-31 (2012)
PMID: 22923517

Function and Biology Details

Reaction catalysed: 
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141582 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Peptidyl-tRNA hydrolase Chains: A, C
Molecule details ›
Chains: A, C
Length: 197 amino acids
Theoretical weight: 21.4 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7D1 (Residues: 1-194; Coverage: 100%)
Gene names: JW1195, b1204, pth
Sequence domains: Peptidyl-tRNA hydrolase
Structure domains: Peptidyl-tRNA hydrolase
tRNA CCA-acceptor Chains: B, D
Molecule details ›
Chains: B, D
Length: 36 nucleotides
Theoretical weight: 11.53 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P61
Unit cell:
a: 55.07Å b: 55.07Å c: 413.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.193 0.237
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Structural and functional insights into peptidyl-tRNA hydrolase.
Sharma et al. (2014)
15 other articles

6 mentions without citation

Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
Ito et al. (2012)
5 more