1H, 13C and 15N resonance assignment of the YTH domain of YTHDC2

Fahu He; Ryuta Endo; Kanako Kuwasako; Mari Takahashi; Kengo Tsuda; Takashi Nagata; Satoru Watanabe; Akiko Tanaka; Naohiro Kobayashi; Takanori Kigawa; Peter Güntert; Mikako Shirouzu; Shigeyuki Yokoyama; Yutaka Muto

doi:10.1007/s12104-020-09974-3

¹H, ¹³C and ¹⁵N resonance assignment of the YTH domain of YTHDC2

Biomol NMR Assign. 2021 Apr;15(1):1-7. doi: 10.1007/s12104-020-09974-3. Epub 2020 Sep 15.

Authors

Fahu He^#^{1

2}, Ryuta Endo^#^{1

2}, Kanako Kuwasako^{1

2

3}, Mari Takahashi^{1

2}, Kengo Tsuda^{1

2}, Takashi Nagata^{1

4

5}, Satoru Watanabe^{1

6}, Akiko Tanaka^{1

2}, Naohiro Kobayashi^{1

7}, Takanori Kigawa^{1

6}, Peter Güntert^{8

9

10}, Mikako Shirouzu^{1

2}, Shigeyuki Yokoyama^{11

12}, Yutaka Muto^{13

14

15}

Affiliations

¹ RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
² RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
³ Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
⁴ Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611 -0011, Japan.
⁵ Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
⁶ RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
⁷ RIKEN SPring-8 Center, Yokohama, 230-0045, Japan.
⁸ Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan.
⁹ Institute of Biophysical Chemistry and Frankfurt Institute of Advanced Studies, Goethe-University Frankfurt, Max- von-Laue-Str.9, 60438, Frankfurt am Main, Germany.
¹⁰ Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan.
¹¹ RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. yokoyama@riken.jp.
¹² RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. yokoyama@riken.jp.
¹³ RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. ymuto@musashino-u.ac.jp.
¹⁴ RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan. ymuto@musashino-u.ac.jp.
¹⁵ Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan. ymuto@musashino-u.ac.jp.

^# Contributed equally.

PMID: 32930954
DOI: 10.1007/s12104-020-09974-3

Abstract

In humans, YTH (YT521-B homology) domain containing protein 2 (YTHDC2) plays a crucial role in the phase-shift from mitosis to meiosis. YTH domains bind to methylated adenosine nucleotides such as m⁶A. In a phylogenic tree, the YTH domain of YTHDC2 (YTH2) and that of the YTH containing protein YTHDC1 (YTH1) belong to the same sub-group. However, the binding affinity of m⁶A differs between these proteins. Here, we report ¹H, ¹³C and ¹⁵N resonance assignment of YTH2 and its solution structure to examine the difference of the structural architecture and the dynamic properties of YTH1 and YTH2. YTH2 adopts a β1-α1-β2-α2-β3-β4-β5-α3-β6-α4 topology, which was also observed in YTH1. However, the β4-β5 loops of YTH1 and YTH2 are distinct in length and amino acid composition. Our data revealed that, unlike in YTH1, the structure of m⁶A-binding pocket of YTH2 formed by the β4-β5 loop is stabilized by electrostatic interaction. This assignment and the structural information for YTH2 will provide the insight on the further functional research of YTHDC2.

Keywords: Meiosis; N6-methylated adenosine; RNA binding domain; Spermatogonium; YTH domain; YTHDC2.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine
Nuclear Magnetic Resonance, Biomolecular*
RNA

Substances

RNA
Adenosine