title: Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate.
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.
authors.affiliation: Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan. matsumura@chem.eng.osaka-u.ac.jp
authors.forename: Hiroyoshi
authors.initials: H
authors.lastname: Matsumura
authors.forename: Eiichi
authors.initials: E
authors.lastname: Mizohata
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ishida
authors.forename: Ayako
authors.initials: A
authors.lastname: Kogami
authors.forename: Takeshi
authors.initials: T
authors.lastname: Ueno
authors.forename: Amane
authors.initials: A
authors.lastname: Makino
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Inoue
authors.forename: Akiho
authors.initials: A
authors.lastname: Yokota
authors.forename: Tadahiko
authors.initials: T
authors.lastname: Mae
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Kai
mesh_terms: D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D005942:Gluconates / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D009249:NADP / Q000737:chemistry / Q000378:metabolism*; D012275:Oryza / Q000201:enzymology* / Q000378:metabolism; D010428:Pentosephosphates / Q000737:chemistry / Q000378:metabolism; D010940:Plant Proteins; D011487:Protein Conformation; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry* / Q000378:metabolism; D013402:Sugar Alcohols / Q000737:chemistry / Q000378:metabolism
chemical_list: D005942:Gluconates; D010428:Pentosephosphates; D010940:Plant Proteins; D013402:Sugar Alcohols; C032687:2-carboxyarabinitol 1,5-biphosphate; D009249:NADP; D012273:Ribulose-Bisphosphate Carboxylase; C008884:6-phosphogluconic acid