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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. (2010)

Bottom Line: Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNA(Phe), and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations.Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown.These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

ABSTRACT
Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNA(Phe), and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations. Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown. Recently, we identified a novel Jumonji C (JmjC)-domain-containing protein, TYW5 (tRNA yW-synthesizing enzyme 5), which forms the OHyW nucleoside by carbon hydroxylation, using Fe(II) ion and 2-oxoglutarate (2-OG) as cofactors. In this work, we present the crystal structures of human TYW5 (hTYW5) in the free and complex forms with 2-OG and Ni(II) ion at 2.5 and 2.8 Å resolutions, respectively. The structure revealed that the catalytic domain consists of a β-jellyroll fold, a hallmark of the JmjC domains and other Fe(II)/2-OG oxygenases. hTYW5 forms a homodimer through C-terminal helix bundle formation, thereby presenting a large, positively charged patch involved in tRNA binding. A comparison with the structures of other JmjC-domain-containing proteins suggested a mechanism for substrate nucleotide recognition. Functional analyses of structure-based mutants revealed the essential Arg residues participating in tRNA recognition by TYW5. These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily.

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Overall structure of hTYW5. (A) and (B) Ribbon representations of the (A) hTYW5 dimer and (B) protomer. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored pink, cyan and yellow, respectively. (C) A secondary structure topology diagram of human TYW5. The α-helices and β-strands are represented by circles and triangles, respectively. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored as in Figures 2A and B. The jellyroll cores of the other 2-OG dependent oxygeneses generally comprise eight β-strands, whereas hTYW5 has only seven strands. The missing β-strand (β8) is represented by the dashed-line triangle.
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Figure 2: Overall structure of hTYW5. (A) and (B) Ribbon representations of the (A) hTYW5 dimer and (B) protomer. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored pink, cyan and yellow, respectively. (C) A secondary structure topology diagram of human TYW5. The α-helices and β-strands are represented by circles and triangles, respectively. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored as in Figures 2A and B. The jellyroll cores of the other 2-OG dependent oxygeneses generally comprise eight β-strands, whereas hTYW5 has only seven strands. The missing β-strand (β8) is represented by the dashed-line triangle.

Mentions: The crystal structure of hTYW5 was determined by the multiwavelength anomalous diffraction (MAD) method, using a selenomethionine-derivatized crystal (Figure 2). We also solved the structure of the cofactor-bound form, by soaking the crystal in buffer containing 2-OG and NiCl2, the latter of which acts as an inhibitor, instead of Fe(II) ion. The final models of the apo and cofactor-bound forms were refined at 2.5 and 2.8 Å resolutions, to free R-factors of 28.1 and 29.9%, respectively (Table 1 and 2). The data collection and refinement statistics are summarized in Table 1 and 2. The root mean square (RMS) deviation between the apo and cofactor-bound forms is 0.31 Å, indicating that they are almost identical.Figure 2.


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. (2010)

Overall structure of hTYW5. (A) and (B) Ribbon representations of the (A) hTYW5 dimer and (B) protomer. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored pink, cyan and yellow, respectively. (C) A secondary structure topology diagram of human TYW5. The α-helices and β-strands are represented by circles and triangles, respectively. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored as in Figures 2A and B. The jellyroll cores of the other 2-OG dependent oxygeneses generally comprise eight β-strands, whereas hTYW5 has only seven strands. The missing β-strand (β8) is represented by the dashed-line triangle.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 2: Overall structure of hTYW5. (A) and (B) Ribbon representations of the (A) hTYW5 dimer and (B) protomer. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored pink, cyan and yellow, respectively. (C) A secondary structure topology diagram of human TYW5. The α-helices and β-strands are represented by circles and triangles, respectively. The N-terminal catalytic domain, the β-jellyroll fold and the C-terminal helix bundle are colored as in Figures 2A and B. The jellyroll cores of the other 2-OG dependent oxygeneses generally comprise eight β-strands, whereas hTYW5 has only seven strands. The missing β-strand (β8) is represented by the dashed-line triangle.
Mentions: The crystal structure of hTYW5 was determined by the multiwavelength anomalous diffraction (MAD) method, using a selenomethionine-derivatized crystal (Figure 2). We also solved the structure of the cofactor-bound form, by soaking the crystal in buffer containing 2-OG and NiCl2, the latter of which acts as an inhibitor, instead of Fe(II) ion. The final models of the apo and cofactor-bound forms were refined at 2.5 and 2.8 Å resolutions, to free R-factors of 28.1 and 29.9%, respectively (Table 1 and 2). The data collection and refinement statistics are summarized in Table 1 and 2. The root mean square (RMS) deviation between the apo and cofactor-bound forms is 0.31 Å, indicating that they are almost identical.Figure 2.

Bottom Line: Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNA(Phe), and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations.Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown.These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

ABSTRACT
Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNA(Phe), and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations. Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown. Recently, we identified a novel Jumonji C (JmjC)-domain-containing protein, TYW5 (tRNA yW-synthesizing enzyme 5), which forms the OHyW nucleoside by carbon hydroxylation, using Fe(II) ion and 2-oxoglutarate (2-OG) as cofactors. In this work, we present the crystal structures of human TYW5 (hTYW5) in the free and complex forms with 2-OG and Ni(II) ion at 2.5 and 2.8 Å resolutions, respectively. The structure revealed that the catalytic domain consists of a β-jellyroll fold, a hallmark of the JmjC domains and other Fe(II)/2-OG oxygenases. hTYW5 forms a homodimer through C-terminal helix bundle formation, thereby presenting a large, positively charged patch involved in tRNA binding. A comparison with the structures of other JmjC-domain-containing proteins suggested a mechanism for substrate nucleotide recognition. Functional analyses of structure-based mutants revealed the essential Arg residues participating in tRNA recognition by TYW5. These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily.

Show MeSH