› 3p1y

X-ray diffraction
2.05Å resolution

Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity

Released:
DOI: 10.2210/pdb3p1y/pdb
PDB entry 3p1y coloured by chain, front view.
PDB entry 3p1y coloured by chain, side view.
PDB entry 3p1y coloured by chain, top view.
Source organisms:
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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128116 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA-splicing endonuclease Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 315 amino acids
Theoretical weight: 37.08 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: O29362 (Residues: 2-173, 179-305; Coverage: 98%)
  • Canonical: Q9YBF1 (Residues: 39-53; Coverage: 8%)
Gene names: AF_0900, APE_1646.1, endA
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 81.77Å b: 104.642Å c: 165.303Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.247 0.287
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

2 mentions without citation

Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex.
Hayne et al. (2022)
1 more