Solution structure of the PWWP domain of the hepatoma-derived growth factor family

Nobukazu Nameki; Naoya Tochio; Seizo Koshiba; Makoto Inoue; Takashi Yabuki; Masaaki Aoki; Eiko Seki; Takayoshi Matsuda; Yukiko Fujikura; Miyuki Saito; Masaomi Ikari; Megumi Watanabe; Takaho Terada; Mikako Shirouzu; Mayumi Yoshida; Hiroshi Hirota; Akiko Tanaka; Yoshihide Hayashizaki; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama

doi:10.1110/ps.04975305

Solution structure of the PWWP domain of the hepatoma-derived growth factor family

Nobukazu Nameki, Naoya Tochio, Seizo Koshiba, Makoto Inoue, Takashi Yabuki, Masaaki Aoki, Eiko Seki, Takayoshi Matsuda, Yukiko Fujikura, Miyuki Saito, Masaomi Ikari, Megumi Watanabe, Takaho Terada, Mikako Shirouzu, Mayumi Yoshida, Hiroshi Hirota, Akiko Tanaka, Yoshihide Hayashizaki, Peter Güntert, Takanori KigawaShigeyuki Yokoyama

Research output: Contribution to journal › Article › peer-review

46 Citations (Scopus)

Abstract

Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded β-barrel with a PWWP-specific long loop connecting β2 and β3 (PR-loop), followed by a helical region including two α-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the β1/β2 loop (β-β arch) and the β3/β4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity.

Original language	English
Pages (from-to)	756-764
Number of pages	9
Journal	Protein Science
Volume	14
Issue number	3
DOIs	https://doi.org/10.1110/ps.04975305
Publication status	Published - 2005 Mar
Externally published	Yes

Keywords

Cavity
HATH region
HDGF
NMR
PR-loop
Protein structure
β-β arch

ASJC Scopus subject areas

Biochemistry
Molecular Biology

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10.1110/ps.04975305

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Nameki, N., Tochio, N., Koshiba, S., Inoue, M., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Fujikura, Y., Saito, M., Ikari, M., Watanabe, M., Terada, T., Shirouzu, M., Yoshida, M., Hirota, H., Tanaka, A., Hayashizaki, Y., Güntert, P., ... Yokoyama, S. (2005). Solution structure of the PWWP domain of the hepatoma-derived growth factor family. Protein Science, 14(3), 756-764. https://doi.org/10.1110/ps.04975305

Nameki, N, Tochio, N, Koshiba, S, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Fujikura, Y, Saito, M, Ikari, M, Watanabe, M, Terada, T, Shirouzu, M, Yoshida, M, Hirota, H, Tanaka, A, Hayashizaki, Y, Güntert, P, Kigawa, T & Yokoyama, S 2005, 'Solution structure of the PWWP domain of the hepatoma-derived growth factor family', Protein Science, vol. 14, no. 3, pp. 756-764. https://doi.org/10.1110/ps.04975305

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abstract = "Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded β-barrel with a PWWP-specific long loop connecting β2 and β3 (PR-loop), followed by a helical region including two α-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the β1/β2 loop (β-β arch) and the β3/β4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity.",

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author = "Nobukazu Nameki and Naoya Tochio and Seizo Koshiba and Makoto Inoue and Takashi Yabuki and Masaaki Aoki and Eiko Seki and Takayoshi Matsuda and Yukiko Fujikura and Miyuki Saito and Masaomi Ikari and Megumi Watanabe and Takaho Terada and Mikako Shirouzu and Mayumi Yoshida and Hiroshi Hirota and Akiko Tanaka and Yoshihide Hayashizaki and Peter G{\"u}ntert and Takanori Kigawa and Shigeyuki Yokoyama",

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doi = "10.1110/ps.04975305",

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AU - Nameki, Nobukazu

AU - Tochio, Naoya

AU - Koshiba, Seizo

AU - Inoue, Makoto

AU - Yabuki, Takashi

AU - Aoki, Masaaki

AU - Seki, Eiko

AU - Matsuda, Takayoshi

AU - Fujikura, Yukiko

AU - Saito, Miyuki

AU - Ikari, Masaomi

AU - Watanabe, Megumi

AU - Terada, Takaho

AU - Shirouzu, Mikako

AU - Yoshida, Mayumi

AU - Hirota, Hiroshi

AU - Tanaka, Akiko

AU - Hayashizaki, Yoshihide

AU - Güntert, Peter

AU - Kigawa, Takanori

AU - Yokoyama, Shigeyuki

PY - 2005/3

Y1 - 2005/3

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AB - Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF and five HDGF-related proteins (HRPs) always have a PWWP domain, which is a module found in many chromatin-associated proteins. In this study, we determined the solution structure of the PWWP domain of HDGF-related protein-3 (HRP-3) by NMR spectroscopy. The structure consists of a five-stranded β-barrel with a PWWP-specific long loop connecting β2 and β3 (PR-loop), followed by a helical region including two α-helices. Its structure was found to have a characteristic solvent-exposed hydrophobic cavity, which is composed of an abundance of aromatic residues in the β1/β2 loop (β-β arch) and the β3/β4 loop. A similar ligand binding cavity occurs at the corresponding position in the Tudor, chromo, and MBT domains, which have structural and probable evolutionary relationships with PWWP domains. These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity.

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Solution structure of the PWWP domain of the hepatoma-derived growth factor family

Abstract

Keywords

ASJC Scopus subject areas

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