title: Structural and functional differences of SWIRM domain subtypes.
abstract: SWIRM is a conserved domain found in several chromatin-associated proteins. Based on their sequences, the SWIRM family members can be classified into three subfamilies, which are represented by Swi3, LSD1, and Ada2. Here we report the SWIRM structure of human MYb-like, Swirm and Mpn domain-containing protein-1 (MYSM1). The MYSM1 SWIRM structure forms a compact HTH-related fold comprising five alpha-helices, which best resembles the Swi3 SWIRM structure, among the known SWIRM structures. The MYSM1 and Swi3 SWIRM structures are more similar to the LSD1 structure than the Ada2alpha structure. The SWIRM domains of MYSM1 and LSD1 lacked DNA binding activity, while those of Ada2alpha and the human Swi3 counterpart, SMARCC2, bound DNA. The dissimilarity in the DNA-binding ability of the MYSM1 and SMARCC2 SWIRM domains might be due to a couple of amino acid differences in the last helix. These results indicate that the SWIRM family has indeed diverged into three structural subfamilies (Swi3/MYSM1, LSD1, and Ada2 types), and that the Swi3/MYSM1-type subfamily has further diverged into two functionally distinct groups. We also solved the structure of the SANT domain of MYSM1, and demonstrated that it bound DNA with a similar mode to that of the c-Myb DNA-binding domain.
authors.affiliation: RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
authors.forename: Misao
authors.initials: M
authors.lastname: Yoneyama
authors.forename: Naoya
authors.initials: N
authors.lastname: Tochio
authors.forename: Takashi
authors.initials: T
authors.lastname: Umehara
authors.forename: Seizo
authors.initials: S
authors.lastname: Koshiba
authors.forename: Makoto
authors.initials: M
authors.lastname: Inoue
authors.forename: Takashi
authors.initials: T
authors.lastname: Yabuki
authors.forename: Masaaki
authors.initials: M
authors.lastname: Aoki
authors.forename: Eiko
authors.initials: E
authors.lastname: Seki
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Matsuda
authors.forename: Satoru
authors.initials: S
authors.lastname: Watanabe
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Tomo
authors.forename: Yuji
authors.initials: Y
authors.lastname: Nishimura
authors.forename: Takushi
authors.initials: T
authors.lastname: Harada
authors.forename: Takaho
authors.initials: T
authors.lastname: Terada
authors.forename: Mikako
authors.initials: M
authors.lastname: Shirouzu
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Osamu
authors.initials: O
authors.lastname: Ohara
authors.forename: Akiko
authors.initials: A
authors.lastname: Tanaka
authors.forename: Takanori
authors.initials: T
authors.lastname: Kigawa
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000595:Amino Acid Sequence; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D012996:Solutions; D013329:Structure-Activity Relationship; D015534:Trans-Activators; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*; D064570:Ubiquitin-Specific Proteases
chemical_list: D004268:DNA-Binding Proteins; C520745:MYSM1 protein, human; D012996:Solutions; D015534:Trans-Activators; D014157:Transcription Factors; D004247:DNA; D064570:Ubiquitin-Specific Proteases