1WRB

Crystal structure of the N-terminal RecA-like domain of DjVLGB, a pranarian Vasa-like RNA helicase

Summary for 1WRB

• Entry DOI: 10.2210/pdb1wrb/pdb
• Descriptor: DjVLGB, SULFATE ION (3 entities in total)
• Functional Keywords: rna helicase, dead box, vasa, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, hydrolase
• Biological source: Dugesia japonica
• Total number of polymer chains: 2
• Total formula weight: 57163.74

Authors

Kurimoto, K.,Muto, Y.,Obayashi, N.,Terada, T.,Shirouzu, M.,Yabuki, T.,Aoki, M.,Seki, E.,Matsuda, T.,Kigawa, T.,Okumura, H.,Tanaka, A.,Shibata, N.,Kashikawa, M.,Agata, K.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-10-14, release date: 2005-04-12, Last modification date: 2024-03-13)

Primary citation

Kurimoto, K.,Muto, Y.,Obayashi, N.,Terada, T.,Shirouzu, M.,Yabuki, T.,Aoki, M.,Seki, E.,Matsuda, T.,Kigawa, T.,Okumura, H.,Tanaka, A.,Shibata, N.,Kashikawa, M.,Agata, K.,Yokoyama, S.
Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein
J.Struct.Biol., 150:58-68, 2005

PubMed Abstract: 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.

PubMed: 15797730
DOI: 10.1016/j.jsb.2005.01.006

Experimental method

X-RAY DIFFRACTION (2.4 Å)