› 5d08

X-ray diffraction
1.75Å resolution

Crystal structure of selenomethionine-labeled epoxyqueuosine reductase

Released:
DOI: 10.2210/pdb5d08/pdb
PDB entry 5d08 coloured by chain, front view.
PDB entry 5d08 coloured by chain, side view.
PDB entry 5d08 coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
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

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161267 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Epoxyqueuosine reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 437 amino acids
Theoretical weight: 49.21 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P97030 (Residues: 2-386; Coverage: 100%)
Gene names: BSU08910, queG, ygaP, yhbA
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand SF4 4 x SF4
Ligand B12 2 x B12
Ligand GOL 2 x GOL
Ligand PO4 2 x PO4
Ligand CL 2 x CL
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 84.301Å b: 95.78Å c: 111.175Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Vitamin B12 in the spotlight again.
Bridwell-Rabb et al. (2017)
8 more

3 mentions without citation

Screening soybean cyst nematode effectors for their ability to suppress plant immunity.
Pogorelko et al. (2020)
2 more