3AXK

Structure of rice Rubisco in complex with NADP(H)

Summary for 3AXK

• Entry DOI: 10.2210/pdb3axk/pdb
• Related: 1WDD 3AXM
• Descriptor: Ribulose bisphosphate carboxylase large chain, Ribulose bisphosphate carboxylase small chain, chloroplastic, GLYCEROL, ... (6 entities in total)
• Functional Keywords: alpha/beta barrel, photosynthetic carbon reduction, lyase
• Biological source: Oryza sativa Japonica Group (Japanese rice); More
• Cellular location: Plastid, chloroplast: P0C512 Q0INY7
• Total number of polymer chains: 4
• Total formula weight: 137832.50

Authors

Matsumura, H.,Mizohata, E.,Ishida, H.,Kogami, A.,Ueno, T.,Makino, A.,Inoue, T.,Yokota, A.,Mae, T.,Kai, Y. (deposition date: 2011-04-11, release date: 2012-04-11, Last modification date: 2013-06-05)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.9 Å)