Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein

• Published in: Journal of structural biology Vol. 150; no. 1; pp. 58 - 68
• Main Authors: Kurimoto, Kazuki, Muto, Yutaka, Obayashi, Naomi, Terada, Takaho, Shirouzu, Mikako, Yabuki, Takashi, Aoki, Masaaki, Seki, Eiko, Matsuda, Takayoshi, Kigawa, Takanori, Okumura, Hiromi, Tanaka, Akiko, Shibata, Norito, Kashikawa, Maki, Agata, Kiyokazu, Yokoyama, Shigeyuki
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-04-2005
• Subjects: Amino Acid Sequence; Animals; Crystal structure; Helminth Proteins - chemistry; Helminth Proteins - classification; Molecular Sequence Data; Molecular Structure; Phylogeny; PL10; Planarians - enzymology; Protein Structure, Tertiary; Rec A Recombinases - chemistry; Rec A Recombinases - classification; RNA helicase; RNA Helicases - chemistry; RNA Helicases - classification; RRM; SH3; RRM; PL10; RNA helicase; Crystal structure; SH3
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2005.01.006

The
Dugesia japonica vasa-like gene B (DjVLGB) protein is a DEAD-box RNA helicase of a planarian, which is well known for its strong regenerative capacity. DjVLGB shares sequence similarity to the
Drosophila germ-line-specific DEAD-box RNA helicase Vasa, and even higher similarity to its paralogue, mouse PL10. In this study, we solved the crystal structure of the DjVLGB N-terminal RecA-like domain. The overall fold and the structures of the putative ATPase active site of the DjVLGB N-terminal RecA-like domain are similar to those of the previously reported DEAD-box RNA helicase structures. In contrast, the surface structure of the side opposite to the putative ATPase active site is different from those of the other DEAD-box RNA helicases; the characteristic hydrophobic pockets are formed with aromatic and proline residues. These pocket-forming residues are conserved in the PL10-subfamily proteins, but less conserved in the Vasa orthologues and not conserved in the DEAD-box RNA helicases. Therefore, the structural features that we found are characteristic of the PL10-subfamily proteins and might contribute to their biological roles in germ-line development.