› 4fz2

X-ray diffraction
2.25Å resolution

Crystal structure of the fourth type of archaeal tRNA splicing endonuclease from Candidatus Micrarchaeum acidiphilum ARMAN-2

Released:
DOI: 10.2210/pdb4fz2/pdb
PDB entry 4fz2 coloured by chain, front view.
PDB entry 4fz2 coloured by chain, side view.
PDB entry 4fz2 coloured by chain, top view.
Source organism: Candidatus Micrarchaeum acidiphilum ARMAN-2
Primary publication:
X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity.
Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H
Nucleic Acids Res 40 10554-66 (2012)
PMID: 22941657

Function and Biology Details

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-111687 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA intron endonuclease catalytic domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 395 amino acids
Theoretical weight: 45.88 KDa
Source organism: Candidatus Micrarchaeum acidiphilum ARMAN-2
Expression system: Escherichia coli
UniProt:
  • Canonical: C7DIA5 (Residues: 1-387; Coverage: 100%)
Gene name: UNLARM2_0797
Sequence domains: tRNA intron endonuclease, catalytic C-terminal domain
Structure domains: tRNA intron endonuclease, N-terminal domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P32
Unit cell:
a: 112.021Å b: 112.021Å c: 81.079Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.218 0.257
Expression system: Escherichia coli

Quick links

Citations

2 review citations

tRNA gene diversity in the three domains of life.
Fujishima et al. (2014)
1 more

4 mentions without citation

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