Journal:MicroPubl Biol:000570

Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN

Ljiljana Sjekloća, Adrian R. Ferré-D’Amaré ^[1]

Molecular Tour
Amidst intriguing complexity of tRNA non canonical bases, wyosine stands out for being the only fluorescent nucleobase. Sequential enzymatic reactions transform specifically phenylalanine tRNA G37 in a tricyclic, highly hydrophobic, hypermodified nucleoside adjacent to the anticodon loop where it may influence anticodon flexibility and translation efficiency.

S-adenosyl-L-methionine-dependent 4-demethylwyosin synthase TYW1 is an iron-sulfur enzyme which merges pyruvate with pyrimidine-imidazole ring of methylated G37 to generate 4-demethylwyosine imG-14, the first tricyclic intermediate in wyosine biosynthesis. In Eukaryotes TYW1 is a two-domain protein which contains a flavodoxin-like domain at its amino-terminus and an iron-sulfur cluster carboxyl-terminal domain. We solved the crystal structure of fungal Tyw1 flavodoxin-like domain in complex with FMN (PDB 6pup and 6puq).

The crystallographic model (PDB 6pup) contains two Mn (II) ions:

• 1st view.
• 2nd view. Rotated ~ 90° clockwise around the vertical axis, respective to the orientation shown at 1st view.
• 3rd view. Rotated ~ 90° clockwise around the horizontal axis, respective to the orientation shown at 1st view.

The crystallographic model (PDB 6pup), electrostatic potential:

• 1st view.
• 2nd view. Rotated ~ 90° clockwise around the vertical axis, respective to the orientation shown at 1st view.
• 3rd view. Rotated ~ 90° clockwise around the horizontal axis, respective to the orientation shown at 1st view.

The crystallographic model (PDB 6pup) contains two Mn (II) ions bridged by a water molecule (salmon and red spheres, respectively).

• 1st view.
• 2nd view after ~180° rotation around the vertical axis.

Remember to drag the structures with the mouse to rotate them.

FMN binding site. FMN is in yellow ball-and-stick representation. The residues contacting FMN, hydrogen bonds (white dashed lines), and selected water molecules (red spheres) are shown. The TYW1 residues are in pink.

Diametrically opposite the FMN binding site there is a system of several loops, the longest of which (residues 168-180) contains Asp168-Phe169-Arg170 and Leu176, residues conserved in all TYW1 proteins. Superposition according to DALI search. This loop is the most structurally dissimilar from the nearest structural homologues identified by a DALI search: eukaryotic NADP(H)-cytochrome 450 diflavin oxidoreductase (3qfc) and nitric-oxide synthase (1tll), and bacterial flavodoxin (5lji) and sulfite reductase NADP(H) flavoprotein (1ykg). The DALI server was used.

TYW1 structural similarity to enzymes which couple FAD/FMN and NADP(H) coenzymes for their activity, together with the presence of an unexpected metal binding site, point to a very complex regulation of TYW1 by cell energy metabolism.

PDB references: 1.9 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN 6pup; 1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN 6puq.

References

1. ↑ Sjekloca L, Ferre-D'Amare AR. Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA (Phe) 4-demethylwyosine synthase Tyw1 in complex with FMN. MicroPubl Biol. 2022 Jun 8;2022. doi: 10.17912/micropub.biology.000570., eCollection 2022. PMID:35693892 doi:http://dx.doi.org/10.17912/micropub.biology.000570