1 H, 13 C and 15 N resonance assignment of the YTH domain of YTHDC2
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ARTICLE
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H, 13C and 15N resonance assignment of the YTH domain of YTHDC2
Fahu He1,2 · Ryuta Endo1,2 · Kanako Kuwasako1,2,3 · Mari Takahashi1,2 · Kengo Tsuda1,2 · Takashi Nagata1,4,5 · Satoru Watanabe1,6 · Akiko Tanaka1,2 · Naohiro Kobayashi1,7 · Takanori Kigawa1,6 · Peter Güntert8,9,10 · Mikako Shirouzu1,2 · Shigeyuki Yokoyama1,11 · Yutaka Muto1,2,3 Received: 11 July 2020 / Accepted: 5 September 2020 © Springer Nature B.V. 2020
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 m 6A. 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 YTH domain · YTHDC2 · RNA binding domain · Spermatogonium · N6-methylated adenosine · Meiosis
The chemical shift assignments for the YTH domain of YTHDC2 have been deposited in the BMRB database with the accession no. 36310. The atomic coordinates for the ensemble of 20 NMR structures of YTH2 calculated by CYANA 2.1 have been deposited in the Protein Data Bank (accession code 2YU6) and those with Amber12 refinement in the Protein Data Bank (accession code 6LR2). Fahu He and Ryuta Endo have contributed equally to this work. Electronic supplementary material The online version of this article (doi:https://doi.org/10.1007/s12104-020-09974-3) contains supplementary material, which is available to authorized users. * Shigeyuki Yokoyama [email protected] * Yutaka Muto ymuto@musashino‑u.ac.jp 1
Biological context In human cells, YTH (YT521-B homology) domain containing protein 2 (YTHDC2) binds to the mRNAs rich with N6-methyladenosines (m6A) along with the meiosis-specific coiled-coil domain-containing protein (MEIOC). Simultaneously, YTHDC2 recruits the 5ʹ–3ʹ exonuclease 1 (XRN1) and interact with the small ribosomal subunit to accelerate the degradation of the modified mitotic mRNAs (Wojtas et al. 2017; Jain et al. 2018; Kretschmer et al. 2018). YTHDC2 is also reportedly involved in stabilization of the 4
Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611 ‑0011, Japan
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Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611‑0011, Japan
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Present Address: RIKEN Quant
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