› 3b0v

X-ray diffraction
3.51Å resolution

tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA

Released:
DOI: 10.2210/pdb3b0v/pdb
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PDB entry 3b0v coloured by chain, front view.
PDB entry 3b0v coloured by chain, side view.
PDB entry 3b0v coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Molecular basis of dihydrouridine formation on tRNA.
Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I
Proc Natl Acad Sci U S A 108 19593-8 (2011)
PMID: 22123979

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:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-290140 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
tRNA-dihydrouridine(20/20a) synthase Chains: C, D
Molecule details ›
Chains: C, D
Length: 363 amino acids
Theoretical weight: 41.42 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SMC7 (Residues: 1-342; Coverage: 100%)
Gene names: TTHA0016, dus
Sequence domains: Dihydrouridine synthase (Dus)
Structure domains:
tRNA Chains: A, B
Molecule details ›
Chains: A, B
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand FMN 2 x FMN
2 modified residues:
Ligand H2U 2 x H2U
Ligand MSE 22 x MSE

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 118.89Å b: 118.89Å c: 319.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.3 0.3 0.32
Expression system: Escherichia coli

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Citations

10 review citations

tRNA Modifications: Impact on Structure and Thermal Adaptation.
Lorenz et al. (2017)
9 more

8 mentions without citation

The diverse structural modes of tRNA binding and recognition.
Biela et al. (2023)
7 more

PDB-REDO

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