› 5d0b

X-ray diffraction
2.64Å resolution

Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified tRNA stem loop

Released:
DOI: 10.2210/pdb5d0b/pdb
PDB entry 5d0b coloured by chain, front view.
PDB entry 5d0b coloured by chain, side view.
PDB entry 5d0b 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:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-161269 (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 BL21(DE3)
UniProt:
  • Canonical: P97030 (Residues: 1-386; Coverage: 100%)
Gene names: BSU08910, queG, ygaP, yhbA
Sequence domains:
RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') Chain: F
Molecule details ›
Chain: F
Length: 17 nucleotides
Theoretical weight: 5.55 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SF4 4 x SF4
Ligand B12 2 x B12
Ligand PO4 2 x PO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P21
Unit cell:
a: 45.644Å b: 110.754Å c: 99.223Å
α: 90° β: 95.16° γ: 90°
R-values:
R R work R free
0.193 0.192 0.221
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 review citations

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

3 mentions without citation

Metabolic functions of the human gut microbiota: the role of metalloenzymes.
Rajakovich et al. (2019)
2 more