› 5oc5

X-ray diffraction
1.89Å resolution

Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD K419A-K420A mutant

Released:
DOI: 10.2210/pdb5oc5/pdb
PDB entry 5oc5 coloured by chain, front view.
PDB entry 5oc5 coloured by chain, side view.
PDB entry 5oc5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2.
Bou-Nader C, Barraud P, Pecqueur L, Pérez J, Velours C, Shepard W, Fontecave M, Tisné C, Hamdane D
Nucleic Acids Res 47 3117-3126 (2019)
PMID: 30605527

Function and Biology Details

Reaction catalysed: 
5,6-dihydrouracil(20) in tRNA + NAD(P)(+) = uracil(20) in tRNA + NAD(P)H
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192677 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like Chain: A
Molecule details ›
Chain: A
Length: 120 amino acids
Theoretical weight: 13.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NX74 (Residues: 338-450; Coverage: 23%)
Gene names: DUS2, DUS2L
Sequence domains: Double-stranded RNA binding motif
Structure domains: Double Stranded RNA Binding Domain

Ligands and Environments

2 bound ligands:
Ligand GOL 3 x GOL
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P41
Unit cell:
a: 36.17Å b: 36.17Å c: 75.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.169 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Naturally occurring modified ribonucleosides.
McCown et al. (2020)
2 more