› 4gcw

X-ray diffraction
3Å resolution

Crystal structure of RNase Z in complex with precursor tRNA(Thr)

Released:
DOI: 10.2210/pdb4gcw/pdb
PDB entry 4gcw coloured by chain, front view.
PDB entry 4gcw coloured by chain, side view.
PDB entry 4gcw coloured by chain, top view.
Source organisms:
Primary publication:
Activation of tRNA maturation by downstream uracil residues in B. subtilis.
Pellegrini O, Li de la Sierra-Gallay I, Piton J, Gilet L, Condon C
Structure 20 1769-77 (2012)
PMID: 22940585

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-157038 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Ribonuclease Z Chain: A
Molecule details ›
Chain: A
Length: 320 amino acids
Theoretical weight: 35.63 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P54548 (Residues: 1-307; Coverage: 100%)
Gene names: BSU23840, rnz, yqjK
Sequence domains: Beta-lactamase superfamily domain
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
TRNA(THR) Chain: B
Molecule details ›
Chain: B
Length: 76 nucleotides
Theoretical weight: 24.6 KDa
Source organism: Bacillus subtilis
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MES 1 x MES
2 modified residues:
Ligand OMU 2 x OMU
Ligand A2M 2 x A2M

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2
Unit cell:
a: 174.08Å b: 42.55Å c: 110.89Å
α: 90° β: 127.18° γ: 90°
R-values:
R R work R free
0.228 0.227 0.256
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

3 review citations

Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA.
Arraiano et al. (2013)
2 more

11 mentions without citation

The tRNA Elbow in Structure, Recognition and Evolution.
Zhang et al. (2016)
10 more