› 3p1z

X-ray diffraction
2.8Å resolution

Crystal structure of the Aperopyrum pernix RNA splicing endonuclease

Released:
DOI: 10.2210/pdb3p1z/pdb
Model geometry
Fit model/data
PDB entry 3p1z coloured by chain, front view.
PDB entry 3p1z coloured by chain, side view.
PDB entry 3p1z coloured by chain, top view.
Source organism: Aeropyrum pernix
Primary publication:
Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop.
Hirata A, Kitajima T, Hori H
OpenAccess logo Nucleic Acids Res 39 9376-89 (2011)
PMID: 21846775

Function and Biology Details

Reaction catalysed: 
PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195451 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Putative uncharacterized protein Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 170 amino acids
Theoretical weight: 18.6 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YE85 (Residues: 1-170; Coverage: 100%)
Gene name: APE_0685
Sequence domains:
Structure domains:
tRNA-splicing endonuclease Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 186 amino acids
Theoretical weight: 20.63 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YBF1 (Residues: 1-186; Coverage: 100%)
Gene names: APE_1646.1, endA
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P31
Unit cell:
a: 135.036Å b: 135.036Å c: 156.246Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.263 0.26 0.318
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea.
Clouet-d'Orval et al. (2018)
3 more

5 mentions without citation

Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases.
Hirata A. (2019)
4 more