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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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Structural comparison of (A) TYW5 with other JmjC-domain-containing proteins, (B) FIH, (C) JMJD2A and Fe(II)/2-OG dependent oxygenase and (D) AlkB. In each panel, the structure is shown in both ribbon and surface models. In the ribbon models in the left column, the core β sheets of the β jellyroll fold are colored orange. The structures were aligned using the SSM algorithm implemented in COOT (32). In the surface models in the right column, the molecular surfaces of the positively charged regions are colored blue and those of the negatively charged regions are colored red, with the intensity of the color proportional to the local potential calculated by the program APBS (35). The bound substrates are shown in stick models. The surfaces around the catalytic pocket are indicated by circles.
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Figure 6: Structural comparison of (A) TYW5 with other JmjC-domain-containing proteins, (B) FIH, (C) JMJD2A and Fe(II)/2-OG dependent oxygenase and (D) AlkB. In each panel, the structure is shown in both ribbon and surface models. In the ribbon models in the left column, the core β sheets of the β jellyroll fold are colored orange. The structures were aligned using the SSM algorithm implemented in COOT (32). In the surface models in the right column, the molecular surfaces of the positively charged regions are colored blue and those of the negatively charged regions are colored red, with the intensity of the color proportional to the local potential calculated by the program APBS (35). The bound substrates are shown in stick models. The surfaces around the catalytic pocket are indicated by circles.

Mentions: The most prevalent JmjC-domain-containing proteins are histone demethylases, which catalyze the hydroxylation of the methyl group of the target methyl-lysine residues in histones, and the unstable hydroxymethyl lysine thus generated is then spontaneously converted into formaldehyde and lysine. The crystal structure of JMJD2A, which is involved in the demethylation of di- and tri-methylated H3K9 and H3K36, was reported (31,32). As expected from the sequence similarity, hTYW5 also has a similar β-jellyroll core structure to that of JMJD2A (Figure 6A and C) (r.m.s.d. = 2.87 Å for 185 Cα atoms). The structural arrangements of the catalytic residues that ligate the Fe(II) and 2-OG cofactors are also well conserved between hTYW5 and JMJD2A. However, the structural similarity to JMJD2A is limited to the core structure, and the surrounding structural elements around the β-jellyroll fold are different. JMJD2A also has an additional α-helical C-terminal domain, but the arrangement of the α helices is completely different from those of both hTYW5 and FIH (Figure 6A, B and C). This is consistent with the fact that this C-terminal domain of JMJD2A is not involved in the dimer formation. Furthermore, the resultant molecular surface and its electrostatic potential around the catalytic pocket are completely different; the catalytic pocket of hTYW5 is positively charged, whereas that of JMJD2A is negatively charged (Figure 6A and C). This is reasonable, because JMJD2A recognizes the positively charged histone tail, whereas hTYW5 binds the negatively charged tRNA.Figure 6.


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)

Structural comparison of (A) TYW5 with other JmjC-domain-containing proteins, (B) FIH, (C) JMJD2A and Fe(II)/2-OG dependent oxygenase and (D) AlkB. In each panel, the structure is shown in both ribbon and surface models. In the ribbon models in the left column, the core β sheets of the β jellyroll fold are colored orange. The structures were aligned using the SSM algorithm implemented in COOT (32). In the surface models in the right column, the molecular surfaces of the positively charged regions are colored blue and those of the negatively charged regions are colored red, with the intensity of the color proportional to the local potential calculated by the program APBS (35). The bound substrates are shown in stick models. The surfaces around the catalytic pocket are indicated by circles.
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Related In: Results  -  Collection

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Show All Figures
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Figure 6: Structural comparison of (A) TYW5 with other JmjC-domain-containing proteins, (B) FIH, (C) JMJD2A and Fe(II)/2-OG dependent oxygenase and (D) AlkB. In each panel, the structure is shown in both ribbon and surface models. In the ribbon models in the left column, the core β sheets of the β jellyroll fold are colored orange. The structures were aligned using the SSM algorithm implemented in COOT (32). In the surface models in the right column, the molecular surfaces of the positively charged regions are colored blue and those of the negatively charged regions are colored red, with the intensity of the color proportional to the local potential calculated by the program APBS (35). The bound substrates are shown in stick models. The surfaces around the catalytic pocket are indicated by circles.
Mentions: The most prevalent JmjC-domain-containing proteins are histone demethylases, which catalyze the hydroxylation of the methyl group of the target methyl-lysine residues in histones, and the unstable hydroxymethyl lysine thus generated is then spontaneously converted into formaldehyde and lysine. The crystal structure of JMJD2A, which is involved in the demethylation of di- and tri-methylated H3K9 and H3K36, was reported (31,32). As expected from the sequence similarity, hTYW5 also has a similar β-jellyroll core structure to that of JMJD2A (Figure 6A and C) (r.m.s.d. = 2.87 Å for 185 Cα atoms). The structural arrangements of the catalytic residues that ligate the Fe(II) and 2-OG cofactors are also well conserved between hTYW5 and JMJD2A. However, the structural similarity to JMJD2A is limited to the core structure, and the surrounding structural elements around the β-jellyroll fold are different. JMJD2A also has an additional α-helical C-terminal domain, but the arrangement of the α helices is completely different from those of both hTYW5 and FIH (Figure 6A, B and C). This is consistent with the fact that this C-terminal domain of JMJD2A is not involved in the dimer formation. Furthermore, the resultant molecular surface and its electrostatic potential around the catalytic pocket are completely different; the catalytic pocket of hTYW5 is positively charged, whereas that of JMJD2A is negatively charged (Figure 6A and C). This is reasonable, because JMJD2A recognizes the positively charged histone tail, whereas hTYW5 binds the negatively charged tRNA.Figure 6.

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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