› 6pup

X-ray diffraction
1.89Å resolution

1.9 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN

Released:
DOI: 10.2210/pdb6pup/pdb
PDB entry 6pup coloured by chain, front view.
PDB entry 6pup coloured by chain, side view.
PDB entry 6pup coloured by chain, top view.
Source organism: Schizosaccharomyces japonicus yFS275
Primary publication:
Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA Phe 4-demethylwyosine synthase Tyw1 in complex with FMN.
Sjekloća L, Ferré-D'Amaré AR
MicroPubl Biol 2022 (2022)
PMID: 35693892

Function and Biology Details

Reaction catalysed: 
N(1)-methylguanine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + L-methionine + 5'-deoxyadenosine + CO(2) + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110349 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA 4-demethylwyosine synthase (AdoMet-dependent) Chain: A
Molecule details ›
Chain: A
Length: 176 amino acids
Theoretical weight: 19.75 KDa
Source organism: Schizosaccharomyces japonicus yFS275
Expression system: Escherichia coli
UniProt:
  • Canonical: B6K6D6 (Residues: 76-251; Coverage: 26%)
Gene names: SJAG_04265, tyw1
Sequence domains: Flavodoxin

Ligands and Environments

2 bound ligands:
Ligand MN 2 x MN
Ligand FMN 1 x FMN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: C2
Unit cell:
a: 62.268Å b: 58.632Å c: 62.52Å
α: 90° β: 118.71° γ: 90°
R-values:
R R work R free
0.175 0.17 0.218
Expression system: Escherichia coli

Quick links

Citations

3 mentions without citation

Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea.
Urbonavičius et al. (2020)
2 more