› 1udn

X-ray diffraction
2.3Å resolution

Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus

Released:
DOI: 10.2210/pdb1udn/pdb
PDB entry 1udn coloured by chain, front view.
PDB entry 1udn coloured by chain, side view.
PDB entry 1udn coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.
Ishii R, Nureki O, Yokoyama S
J Biol Chem 278 32397-404 (2003)
PMID: 12746447

Function and Biology Details

Reaction catalysed: 
tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130426 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonuclease PH Chain: A
Molecule details ›
Chain: A
Length: 255 amino acids
Theoretical weight: 28.41 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O67069 (Residues: 1-255; Coverage: 100%)
Gene names: aq_924, rnpH, rph
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P6322
Unit cell:
a: 145.441Å b: 145.441Å c: 82.484Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.233 0.233 0.275
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Messenger RNA turnover in eukaryotes: pathways and enzymes.
Meyer et al. (2004)
9 more

3 mentions without citation

The eukaryotic RNA exosome.
Januszyk et al. (2014)
2 more