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Yoshihiro Nakamura,
Takashi Umehara, Hiroaki Hamana,
Yoshihide Hayashizaki,
Makoto Inoue,
Takanori Kigawa,
Mikako Shirouzu,
Takaho Terada,
Akiko Tanaka,
Balasundaram Padmanabhan,
Shigeyuki Yokoyama
[show abstract]
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ABSTRACT: The Wnt/beta-catenin signaling pathway plays important roles in animal development and cancer. Pygopus (Pygo) and Legless (Lgs) are recently discovered core components of the Wnt/beta-catenin transcription machinery complex, and are crucially involved in the regulation of the transcription of the Arm/beta-catenin and T cell factors (TCF). Lgs/Bcl9 functions as an adaptor between Pygo and Arm/beta-catenin. Here, we report the first crystal structure of the plant homeodomain (PHD) finger of Pygopus (Pygo1 PHD), a Pygo family member, which is essential for the association with Lgs/Bcl9. The Pygo1 PHD structure forms a canonical PHD finger motif, stabilized by two Zn ions coordinated in a cross-brace scheme. Surprisingly, the Pygo1 PHD domain forms a dimer in both the crystals and solution. This is the first structural evidence for dimerization among the known PHD domain structures. The dimer formation occurs by the interactions of antiparallel beta-sheets between the symmetry-related beta3 strands of the monomers. The Pygo1 PHD dimer interface mainly comprises hydrophobic residues. Interestingly, some of the interface residues, such as Met372, Thr373, Ala376 and Leu380, are reportedly important for the association with Lgs/Bcl9 and are also critical for transcriptional activation. The M372A and L380D mutants, and several surrounding mutants such as S385A and A386D, showed decreased ability to form dimers and to interact with the homology domain 1 (HD1) of Lgs/Bcl9. These results suggest that the Pygo1 PHD dimerization is functionally important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway.
Journal of Molecular Biology 07/2007; 370(1):80-92. · 4.00 Impact Factor
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Yoshihiro Nakamura,
Takashi Umehara,
Kazumi Nakano,
Moon Kyoo Jang,
Mikako Shirouzu,
Satoshi Morita,
Hiroko Uda-Tochio, Hiroaki Hamana,
Takaho Terada,
Naruhiko Adachi,
Takehisa Matsumoto,
Akiko Tanaka,
Masami Horikoshi,
Keiko Ozato,
Balasundaram Padmanabhan,
Shigeyuki Yokoyama
[show abstract]
[hide abstract]
ABSTRACT: The BET (bromodomains and extra terminal domain) family proteins recognize acetylated chromatin through their bromodomain and act as transcriptional activators. One of the BET proteins, BRD2, associates with the transcription factor E2F, the mediator components CDK8 and TRAP220, and RNA polymerase II, as well as with acetylated chromatin during mitosis. BRD2 contains two bromodomains (BD1 and BD2), which are considered to be responsible for binding to acetylated chromatin. The BRD2 protein specifically recognizes the histone H4 tail acetylated at Lys12. Here, we report the crystal structure of the N-terminal bromodomain (BD1, residues 74-194) of human BRD2. Strikingly, the BRD2 BD1 protein forms an intact dimer in the crystal. This is the first observation of a homodimer among the known bromodomain structures, through the buried hydrophobic core region at the interface. Biochemical studies also demonstrated BRD2 BD1 dimer formation in solution. The two acetyllysine-binding pockets and a negatively charged secondary binding pocket, produced at the dimer interface in BRD2 BD1, may be the unique features that allow BRD2 BD1 to selectively bind to the acetylated H4 tail.
Journal of Biological Chemistry 03/2007; 282(6):4193-201. · 4.77 Impact Factor
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Yoshihiro Nakamura,
Takashi Umehara,
Kazumi Nakano,
Moon Kyoo Jang,
Mikako Shirouzu,
Satoshi Morita,
Hiroko Uda-Tochio, Hiroaki Hamana,
Takaho Terada,
Naruhiko Adachi,
Takehisa Matsumoto,
Akiko Tanaka,
Masami Horikoshi,
Keiko Ozato,
Balasundaram Padmanabhan,
Shigeyuki Yokoyama
[show abstract]
[hide abstract]
ABSTRACT: The BET (bromodomains and extra terminal domain) family proteins recognize acetylated chromatin through their bromodomain and act as transcriptional activators.
One of the BET proteins, BRD2, associates with the transcription factor E2F, the mediator components CDK8 and TRAP220, and
RNA polymerase II, as well as with acetylated chromatin during mitosis. BRD2 contains two bromodomains (BD1 and BD2), which
are considered to be responsible for binding to acetylated chromatin. The BRD2 protein specifically recognizes the histone
H4 tail acetylated at Lys12. Here, we report the crystal structure of the N-terminal bromodomain (BD1, residues 74-194) of human BRD2. Strikingly, the
BRD2 BD1 protein forms an intact dimer in the crystal. This is the first observation of a homodimer among the known bromodomain
structures, through the buried hydrophobic core region at the interface. Biochemical studies also demonstrated BRD2 BD1 dimer
formation in solution. The two acetyllysine-binding pockets and a negatively charged secondary binding pocket, produced at
the dimer interface in BRD2 BD1, may be the unique features that allow BRD2 BD1 to selectively bind to the acetylated H4 tail.
Journal of Biological Chemistry 02/2007; 282(6):4193-4201. · 4.77 Impact Factor
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[show abstract]
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ABSTRACT: TT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 A crystal structure of TT1426 has been determined by the multiwavelength anomalous dispersion (MAD) method. TT1426 comprises a core domain consisting of a central five-stranded beta sheet surrounded by four alpha-helices, and a subdomain in the C terminus. The core domain structure resembles those of the type I PRTase family proteins, although a significant structural difference exists in an inserted 43-residue region. The C-terminal subdomain corresponds to the "hood," which contains a substrate-binding site in the type I PRTases. The hood structure of TT1426 differs from those of the other type I PRTases, suggesting the possibility that TT1426 binds an unknown substrate. The structure-based sequence alignment provides clues about the amino acid residues involved in catalysis and substrate binding.
Protein Science 04/2005; 14(3):823-7. · 2.80 Impact Factor
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Takuma Kasai,
Makoto Inoue,
Seizo Koshiba,
Takashi Yabuki,
Masaaki Aoki,
Emi Nunokawa,
Eiko Seki,
Takayoshi Matsuda,
Natsuko Matsuda,
Yasuko Tomo, [......],
Hiroshi Hirota,
Yo Matsuo,
Kazutoshi Tani,
Harukazu Suzuki,
Takahiro Arakawa,
Piero Carninci,
Jun Kawai,
Yoshihide Hayashizaki,
Takanori Kigawa,
Shigeyuki Yokoyama
[show abstract]
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ABSTRACT: The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is still unknown. Here we determined the structure of a mouse BolA-like protein. The overall topology is alphabetabetaalphaalphabetaalpha, in which beta(1) and beta(2) are antiparallel, and beta(3) is parallel to beta(2). This fold is similar to the class II KH fold, except for the absence of the GXXG loop, which is well conserved in the KH fold. The conserved residues in the BolA-like proteins are assembled on the one side of the protein.
Protein Science 03/2004; 13(2):545-8. · 2.80 Impact Factor
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Noriko Handa,
Takaho Terada,
Yuki Kamewari, Hiroaki Hamana,
Jeremy R H Tame,
Sam-Yong Park,
Kengo Kinoshita,
Motonori Ota,
Haruki Nakamura,
Seiki Kuramitsu,
Mikako Shirouzu,
Shigeyuki Yokoyama
[show abstract]
[hide abstract]
ABSTRACT: The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of TT1542 are present in a wide range of organisms. The TT1542 homologs in eukaryotes, PIG-L in mammals, and GPI12 in yeast and protozoa, have N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI) de-N-acetylase activity. Although most of the homologs in prokaryotes are hypothetical and have no known function, Rv1082 and Rv1170 from Mycobacterium tuberculosis are enzymes involved in the mycothiol detoxification pathway. Here we report the crystal structure of the TT1542 protein at 2.0 A resolution, which represents the first structure for this superfamily of proteins. The structure of the TT1542 monomer consists of a twisted beta-sheet composed of six parallel beta-strands and one antiparallel beta-strand (with the strand order 3-2-1-4-5-7-6) sandwiched between six alpha-helices. The N-terminal five beta-strands and four alpha-helices form an incomplete Rossmann fold-like structure. The structure shares some similarity to the sugar-processing enzymes with Rossmann fold-like domains, especially those of the GPGTF (glycogen phosphorylase/glycosyl transferase) superfamily, and also to the NAD(P)-binding Rossmann fold domains. TT1542 is a homohexamer in the crystal and in solution, the six monomers forming a cylindrical structure. Putative active sites are suggested by the structure and conserved amino acid residues.
Protein Science 09/2003; 12(8):1621-32. · 2.80 Impact Factor
