› 5t8y

X-ray diffraction
2.65Å resolution

Structure of epoxyqueuosine reductase from Bacillus subtilis with the Asp134 catalytic loop swung out of the active site.

Released:
DOI: 10.2210/pdb5t8y/pdb
PDB entry 5t8y coloured by chain, front view.
PDB entry 5t8y coloured by chain, side view.
PDB entry 5t8y coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis of cobalamin-dependent RNA modification.
Dowling DP, Miles ZD, Köhrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL
Nucleic Acids Res 44 9965-9976 (2016)
PMID: 27638883

Function and Biology Details

Reaction catalysed: 
Queuosine(34) in tRNA + acceptor + H(2)O = epoxyqueuosine(34) in tRNA + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161270 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Epoxyqueuosine reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 437 amino acids
Theoretical weight: 48.74 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: P97030 (Residues: 1-386; Coverage: 100%)
Gene names: BSU08910, queG, ygaP, yhbA
Sequence domains:
RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') Chain: X
Molecule details ›
Chain: X
Length: 17 nucleotides
Theoretical weight: 5.43 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SF4 4 x SF4
Ligand B12 2 x B12
Ligand PO4 7 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 44.763Å b: 111.03Å c: 95.971Å
α: 90° β: 99.13° γ: 90°
R-values:
R R work R free
0.239 0.238 0.266
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

A New Facet of Vitamin B12: Gene Regulation by Cobalamin-Based Photoreceptors.
Padmanabhan et al. (2017)
8 more

2 mentions without citation

A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences.
Agarwal et al. (2022)
1 more