Solution structure of the RWD domain of the mouse GCN2 protein

• Published in: Protein science Vol. 13; no. 8; pp. 2089 - 2100
• Main Authors: Nameki, Nobukazu, Yoneyama, Misao, Koshiba, Seizo, Tochio, Naoya, Inoue, Makoto, Seki, Eiko, Matsuda, Takayoshi, Tomo, Yasuko, Harada, Takushi, Saito, Kohei, Kobayashi, Naohiro, Yabuki, Takashi, Aoki, Masaaki, Nunokawa, Emi, Matsuda, Natsuko, Sakagami, Noriko, Terada, Takaho, Shirouzu, Mikako, Yoshida, Mayumi, Hirota, Hiroshi, Osanai, Takashi, Tanaka, Akiko, Arakawa, Takahiro, Carninci, Piero, Kawai, Jun, Hayashizaki, Yoshihide, Kinoshita, Kengo, Güntert, Peter, Kigawa, Takanori, Yokoyama, Shigeyuki
• Format: Journal Article
• Language: English
• Published: Bristol Cold Spring Harbor Laboratory Press 01.08.2004
• Subjects: Amino Acid Sequence; Animals; eIF-2 Kinase - chemistry; GI domain; hydrogen bond network; Mice; Molecular Sequence Data; NMR; Nuclear Magnetic Resonance, Biomolecular; protection factor; Protein Kinases - chemistry; protein structure; Protein Structure, Secondary; Protein Structure, Tertiary; Protein-Serine-Threonine Kinases; Sequence Alignment; Structural Homology, Protein
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1110/ps.04751804

GCN2 is the α‐subunit of the only translation initiation factor (eIF2α) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N‐terminus, which is termed the RWD domain after three major RWD‐containing proteins: RING finger‐containing proteins, WD‐repeat‐containing proteins, and yeast DEAD (DEXD)‐like helicases. In this study, we determined the solution structure of the mouse GCN2 RWD domain using NMR spectroscopy. The structure forms an α + β sandwich fold consisting of two layers: a four‐stranded antiparallel β‐sheet, and three side‐by‐side α‐helices, with an αββββαα topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive β‐turns that overlap with each other by two residues (triple β‐turn). As putative binding sites with GCN1, a structure‐based alignment allowed the identification of several surface residues in α‐helix 3 that are characteristic of the GCN2 RWD domains. Despite the apparent absence of sequence similarity, the RWD structure significantly resembles that of ubiquitin‐conjugating enzymes (E2s), with most of the structural differences in the region connecting β‐strand 4 and α‐helix 3. The structural architecture, including the triple β‐turn, is fundamentally common among various RWD domains and E2s, but most of the surface residues on the structure vary. Thus, it appears that the RWD domain is a novel structural domain for protein‐binding that plays specific roles in individual RWD‐containing proteins.