› 2zyz

X-ray diffraction
1.7Å resolution

Pyrobaculum aerophilum splicing endonuclease

Released:
DOI: 10.2210/pdb2zyz/pdb
PDB entry 2zyz coloured by chain, front view.
PDB entry 2zyz coloured by chain, side view.
PDB entry 2zyz coloured by chain, top view.
Source organism: Pyrobaculum aerophilum
Primary publication:
Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease.
Yoshinari S, Shiba T, Inaoka DK, Itoh T, Kurisu G, Harada S, Kita K, Watanabe Y
Nucleic Acids Res 37 4787-98 (2009)
PMID: 19515941

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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187415 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Putative uncharacterized protein PAE0789 Chains: A, C
Molecule details ›
Chains: A, C
Length: 116 amino acids
Theoretical weight: 13.32 KDa
Source organism: Pyrobaculum aerophilum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZYG6 (Residues: 1-96; Coverage: 100%)
Gene name: PAE0789
Structure domains: Trna Endonuclease; Chain: A, domain 1
tRNA-splicing endonuclease Chains: B, D
Molecule details ›
Chains: B, D
Length: 183 amino acids
Theoretical weight: 20.81 KDa
Source organism: Pyrobaculum aerophilum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZVI1 (Residues: 1-183; Coverage: 100%)
Gene names: PAE2269, endA
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 69.762Å b: 70.726Å c: 131.024Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.252
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Handling tRNA introns, archaeal way and eukaryotic way.
Yoshihisa T. (2014)
4 more

5 mentions without citation

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