Solution structure of the RWD domain of the mouse GCN2 protein.
GCN2 is the alpha-subunit of the only translation initiation factor (eIF2alpha) 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 alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices, with an alphabetabetabetabetaalphaalpha topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive beta-turns that overlap with each other by two residues (triple beta-turn). As putative binding sites with GCN1, a structure-based alignment allowed the identification of several surface residues in alpha-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 beta-strand 4 and alpha-helix 3. The structural architecture, including the triple beta-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.
Nameki
Nobukazu
N
RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan.
Yoneyama
Misao
M
Koshiba
Seizo
S
Tochio
Naoya
N
Inoue
Makoto
M
Seki
Eiko
E
Matsuda
Takayoshi
T
Tomo
Yasuko
Y
Harada
Takushi
T
Saito
Kohei
K
Kobayashi
Naohiro
N
Yabuki
Takashi
T
Aoki
Masaaki
M
Nunokawa
Emi
E
Matsuda
Natsuko
N
Sakagami
Noriko
N
Terada
Takaho
T
Shirouzu
Mikako
M
Yoshida
Mayumi
M
Hirota
Hiroshi
H
Osanai
Takashi
T
Tanaka
Akiko
A
Arakawa
Takahiro
T
Carninci
Piero
P
Kawai
Jun
J
Hayashizaki
Yoshihide
Y
Kinoshita
Kengo
K
Güntert
Peter
P
Kigawa
Takanori
T
Yokoyama
Shigeyuki
S
D000595:Amino Acid Sequence; D000818:Animals; D051379:Mice; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011494:Protein Kinases / Q000737:chemistry*; D017346:Protein Serine-Threonine Kinases; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D019892:eIF-2 Kinase / Q000737:chemistry
D011494:Protein Kinases; C070634:Eif2ak4 protein, mouse; D017346:Protein Serine-Threonine Kinases; D019892:eIF-2 Kinase