Structural and Functional Differences of SWIRM Domain Subtypes

Misao Yoneyama, Naoya Tochio, Takashi Umehara, Seizo Koshiba, Makoto Inoue, Takashi Yabuki, Masaaki Aoki, Eiko Seki, Takayoshi Matsuda, Satoru Watanabe, Yasuko Tomo, Yuji Nishimura, Takushi Harada, Takaho Terada, Mikako Shirouzu, Yoshihide Hayashizaki, Osamu Ohara, Akiko Tanaka, Takanori Kigawa, Shigeyuki Yokoyama

Research output: Contribution to journalArticlepeer-review

39 Citations (Scopus)


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 α-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 Ada2α structure. The SWIRM domains of MYSM1 and LSD1 lacked DNA binding activity, while those of Ada2α 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.

Original languageEnglish
Pages (from-to)222-238
Number of pages17
JournalJournal of Molecular Biology
Issue number1
Publication statusPublished - 2007 May 25


  • chromatin
  • evolution
  • histone
  • Pfam
  • solution structure


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