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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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The proposed tRNAPhe recognition mechanism by TYW5. (A) The electrostatic surface potential of hTYW5. The colors of the molecular surfaces of the positively charged regions are based on the local electrostatic potential, calculated by the program APBS (35). (B) Docking model of TYW5 and tRNAPhe. The tRNA molecule is colored yellow. In (A) and (B), the catalytic pocket, the C-terminal helix bundle and the positively charged patch are indicated by circles.
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Figure 7: The proposed tRNAPhe recognition mechanism by TYW5. (A) The electrostatic surface potential of hTYW5. The colors of the molecular surfaces of the positively charged regions are based on the local electrostatic potential, calculated by the program APBS (35). (B) Docking model of TYW5 and tRNAPhe. The tRNA molecule is colored yellow. In (A) and (B), the catalytic pocket, the C-terminal helix bundle and the positively charged patch are indicated by circles.

Mentions: The surface electrostatic potential of hTYW5 revealed the existence of a large, positively charged patch around the catalytic pocket (Figure 7A), formed by highly conserved, basic residues. In contrast, the catalytic pockets of the other Jmj-C-containing proteins that interact with polypeptides are not positively charged (Figure 6A, B and C). Therefore, the positively charged catalytic pocket of hTYW5 may be involved in the recognition of the tRNA anticodon stem loop, to orient nucleotide 37 correctly within the catalytic site. In addition, a large, positively charged patch exists on the C-terminal helix bundle, which is created by the conserved basic residues (Lys274, Lys281 and Arg284) of the αG helices of both protomers upon dimer formation (Figure 7A). We hypothesize that this positively charged patch on the C-terminal helix bundle is involved in tRNA binding. Based on the present structure and functional analyses, we created a docking model of the TYW5–tRNAPhe complex, in which the D arm is captured by the positively charged patch (Figure 7B), and the anticodon loop is directed into the positively charged catalytic pocket. Further clarification of the mechanism of tRNAPhe recognition by hTYW5 must await the structure determination of the TYW5–tRNAPhe complex.Figure 7.


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)

The proposed tRNAPhe recognition mechanism by TYW5. (A) The electrostatic surface potential of hTYW5. The colors of the molecular surfaces of the positively charged regions are based on the local electrostatic potential, calculated by the program APBS (35). (B) Docking model of TYW5 and tRNAPhe. The tRNA molecule is colored yellow. In (A) and (B), the catalytic pocket, the C-terminal helix bundle and the positively charged patch are indicated by circles.
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Related In: Results  -  Collection

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Figure 7: The proposed tRNAPhe recognition mechanism by TYW5. (A) The electrostatic surface potential of hTYW5. The colors of the molecular surfaces of the positively charged regions are based on the local electrostatic potential, calculated by the program APBS (35). (B) Docking model of TYW5 and tRNAPhe. The tRNA molecule is colored yellow. In (A) and (B), the catalytic pocket, the C-terminal helix bundle and the positively charged patch are indicated by circles.
Mentions: The surface electrostatic potential of hTYW5 revealed the existence of a large, positively charged patch around the catalytic pocket (Figure 7A), formed by highly conserved, basic residues. In contrast, the catalytic pockets of the other Jmj-C-containing proteins that interact with polypeptides are not positively charged (Figure 6A, B and C). Therefore, the positively charged catalytic pocket of hTYW5 may be involved in the recognition of the tRNA anticodon stem loop, to orient nucleotide 37 correctly within the catalytic site. In addition, a large, positively charged patch exists on the C-terminal helix bundle, which is created by the conserved basic residues (Lys274, Lys281 and Arg284) of the αG helices of both protomers upon dimer formation (Figure 7A). We hypothesize that this positively charged patch on the C-terminal helix bundle is involved in tRNA binding. Based on the present structure and functional analyses, we created a docking model of the TYW5–tRNAPhe complex, in which the D arm is captured by the positively charged patch (Figure 7B), and the anticodon loop is directed into the positively charged catalytic pocket. Further clarification of the mechanism of tRNAPhe recognition by hTYW5 must await the structure determination of the TYW5–tRNAPhe complex.Figure 7.

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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