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Protein Science (2007), 16:1577-1587. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Solution structure of the zinc finger HIT domain in protein FON

Fahu He1, Takashi Umehara1, Kengo Tsuda1, Makoto Inoue1, Takanori Kigawa1,2, Takayoshi Matsuda1, Takashi Yabuki1, Masaaki Aoki1, Eiko Seki1, Takaho Terada1, Mikako Shirouzu1, Akiko Tanaka1, Sumio Sugano3, Yutaka Muto1, and Shigeyuki Yokoyama1,4

1 RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
2 Tokyo Institute of Technology, Midori-ku, Yokohama 226-8502, Japan
3 Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
4 Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan

(RECEIVED December 4, 2006; FINAL REVISION May 22, 2007; ACCEPTED May 23, 2007)

The zinc finger HIT domain is a sequence motif found in many proteins, including thyroid hormone receptor interacting protein 3 (TRIP-3), which is possibly involved in maturity-onset diabetes of the young (MODY). Novel zinc finger motifs are suggested to play important roles in gene regulation and chromatin remodeling. Here, we determined the high-resolution solution structure of the zinc finger HIT domain in ZNHIT2 (protein FON) from Homo sapiens, by an NMR method based on 567 upper distance limits derived from NOE intensities measured in three-dimensional NOESY spectra. The structure yielded a backbone RMSD to the mean coordinates of 0.19 Å for the structured residues 12–48. The fold consists of two consecutive antiparallel beta-sheets and two short C-terminal helices packed against the second beta-sheet, and binds two zinc ions. Both zinc ions are coordinated tetrahedrally via a CCCC-CCHC motif to the ligand residues of the zf-HIT domain in an interleaved manner. The tertiary structure of the zinc finger HIT domain closely resembles the folds of the B-box, RING finger, and PHD domains with a cross-brace zinc coordination mode, but is distinct from them. The unique three-dimensional structure of the zinc finger HIT domain revealed a novel zinc-binding fold, as a new member of the treble clef domain family. On the basis of the structural data, we discuss the possible functional roles of the zinc finger HIT domain.

Keywords: NMR; structural genomics; solution structure; zinc finger HIT (zf-HIT); ZNHIT2 (protein FON); thyroid hormone receptor interacting protein 3 (TRIP-3, ZNHIT3)


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