1WDD

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

1WDD の概要

• エントリーDOI: 10.2210/pdb1wdd/pdb
• 分子名称: Ribulose bisphosphate carboxylase large chain, Ribulose bisphosphate carboxylase small chain C, MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: rubisco, photosynthesis, alpha/beta barrel, n-methylmethionine, post-translational modification, lyase
• 由来する生物種: Oryza sativa Japonica Group (Japanese rice); 詳細
• 細胞内の位置: Plastid, chloroplast: P0C512 Q0INY7
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 138273.11

構造登録者

Mizohata, E.,Matsumura, H.,Ueno, T.,Ishida, H.,Inoue, T.,Makino, A.,Mae, T.,Kai, Y. (登録日: 2004-05-13, 公開日: 2004-11-13, 最終更新日: 2023-11-15)

主引用文献

Matsumura, H.,Mizohata, E.,Ishida, H.,Kogami, A.,Ueno, T.,Makino, A.,Inoue, T.,Yokota, A.,Mae, T.,Kai, Y.
Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
J.Mol.Biol., 422:75-86, 2012

PubMed Abstract: The key enzyme of plant photosynthesis, D-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg(2+) coordination. Many biochemical studies have reported that reduced nicotinamide adenine dinucleotide phosphate (NADPH) and 6-phosphogluconate (6PG) function as positive effectors to promote activation. However, the structural mechanism remains unknown. Here, we have determined the crystal structures of activated rice Rubisco in complex with NADPH, 6PG, or 2-carboxy-D-arabinitol 1,5-bisphosphate (2CABP). The structures of the NADPH and 6PG complexes adopt open-state conformations, in which loop 6 at the catalytic site and some other loops are disordered. The structure of the 2CABP complex is in a closed state, similar to the previous 2CABP-bound activated structures from other sources. The catalytic sites of the NADPH and 6PG complexes are fully activated, despite the fact that bicarbonate (NaHCO(3)) was not added into the crystallization solution. In the catalytic site, NADPH does not interact with Mg(2+) directly but interacts with Mg(2+)-coordinated water molecules, while 6PG interacts with Mg(2+) directly. These observations suggest that the two effectors promote Rubisco activation by stabilizing the complex of Mg(2+) and the carbamylated Lys201 with unique interactions and preventing its dissociation. The structure also reveals that the relaxed complex of the effectors (NADPH or 6PG), distinct from the tight-binding mode of 2CABP, would allow rapid exchange of the effectors in the catalytic sites by substrate D-ribulose 1,5-bisphosphate for catalysis in physiological conditions.

PubMed: 22609438
DOI: 10.1016/j.jmb.2012.05.014

実験手法

X-RAY DIFFRACTION (1.35 Å)