› 3al6

X-ray diffraction
2.8Å resolution

Crystal structure of Human TYW5

Released:
DOI: 10.2210/pdb3al6/pdb
PDB entry 3al6 coloured by chain, front view.
PDB entry 3al6 coloured by chain, side view.
PDB entry 3al6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.
Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O
Nucleic Acids Res 39 1576-85 (2011)
PMID: 20972222

Function and Biology Details

Reaction catalysed: 
7-(3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) + 2-oxoglutarate + O(2) = 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106957 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA wybutosine-synthesizing protein 5 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 338 amino acids
Theoretical weight: 39.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A2RUC4 (Residues: 1-315; Coverage: 100%)
Gene names: C2orf60, TYW5
Sequence domains: Cupin-like domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NI 4 x NI
Ligand AKG 2 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P41212
Unit cell:
a: 165.871Å b: 165.871Å c: 105.951Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.24 0.295
Expression system: Escherichia coli

Quick links

Citations

12 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
11 more

9 mentions without citation

Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses.
Gao et al. (2018)
8 more